Practical application of the linkage disequilibrium method for estimating contemporary effective population size: A review

The method to estimate contemporary effective population size (Ne ) based on patterns of linkage disequilibrium (LD) at unlinked loci has been widely applied to natural and managed populations. The underlying model makes many simplifying assumptions, most of which have been evaluated in numerous studies published over the last two decades. Here, these performance evaluations are reviewed and summarized, with a focus on information that facilitates practical application to real populations in nature. Potential sources of bias that are discussed include calculation of r2 (a measure of LD), adjustments for sampling error, physical linkage, age structure, migration and spatial structure, mutation and selection, mating systems, changes in abundance, rare alleles, missing data, genotyping errors, data filtering choices and methods for combining multiple Ne estimates. Factors that affect precision are reviewed, including pseudoreplication that limits the information gained from large genomics datasets, constraints imposed by small samples of individuals, and the challenges in obtaining robust estimates for large populations. Topics that merit further research include the potential to weight r2 values by allele frequency, lump samples of individuals, use genotypic likelihoods rather than called genotypes, prune large LD values and apply the method to species practising partial monogamy.

Are multi-detector computed tomography and cone-beam computed tomography exams and software accurate to measure the upper airway? A systematic review

BACKGROUND

Cone-beam computed tomography (CBCT) has several applications in various fields of dental medicine such as diagnosis and treatment planning. When compared to computed tomography (CT), CBCT's radiation exposure dose is decreased by 3%-20%. However, CBCT produces more scattered signals and may present poorer image quality when compared to medical CT.

OBJECTIVES

To review the findings regarding the accuracy of multi-detector computed tomography (MDCT) and CBCT and to compare the different software programs that segment the upper airway.

SEARCH METHODS

Three databases (PubMed, Medline, and Web of Science) were searched for articles and a manual search was performed.

SELECTION CRITERIA

The inclusion criteria were defined following the PICO framework: P-any patient with a CBCT or CT; I-dimensional evaluation of the upper airway using MDCT or CBCT; C-phantoms; O-the primary outcome was MDCT and CBCT accuracy, the secondary outcome was the evaluation and comparison of software programs used to segment the upper airway.

DATA COLLECTION AND ANALYSIS

Articles that met eligibility criteria were assessed using the Critical Appraisal Skills Program Checklist.

RESULTS

Among the 16 eligible studies, 6 articles referred to the accuracy of MDCTs or CBCTs and 10 to the accuracy of the software. Most articles were qualified as high quality.

CONCLUSIONS

MDCT and CBCT scans' accuracy in upper airway dimensional measurements depends on machine brand, parameters, and segmentation technique. Regarding the segmentation technique, 12 programs were studied. Most either underestimated or overestimated upper airway measurements. In particular, OnDemand3D and INVIVO showed poor accuracy. On the contrary, Invesalius, and MIMICS were accurate in assessing nasal cavities when using an interactive threshold. However, results varied due to methodological differences among the studies. Finally, fully automatic segmentation based on artificial intelligence may represent the future of airway segmentation because it is faster and seems to be accurate. However, further studies are necessary.

REGISTRATION

This study was registered in Prospero (International Prospective Register of Systematic Reviews) with the ID number CRD42022373998.

The diagnostic performance of the Java-based software colorization tool in the diagnosis of dental caries: an in vitro study

OBJECTIVE

This in vitro study aimed to compare the diagnostic outcomes of caries detection in premolar and molar teeth on digital periapical radiographs viewed as grayscale images and in the Java-based software (JBS) pseudocolor spectrum.

METHOD AND MATERIALS

The study comprised 92 premolar or molar human teeth (n = 46 with caries and n = 46 without clinical caries). For each tooth, digital periapical radiographic images (DPRIs), JBS pseudocolor images, and stereomicroscope images were collected, and caries presence and depth were recorded. In JBS pseudocolor images, regions of interest (ROIs) were detected, and ROI values for caries area (ROI1), non-caries area (ROI2), mesial area (ROI3), and distal area (ROI4) were obtained. The degree of inter-observer agreement was determined using the kappa coefficient, and the sensitivity and specificity of the methods were assessed using ROC analysis.

RESULTS

While neither method was consistent with stereomicroscopy in determining caries depth (P < .005), for both observers the kappa value of JBS pseudocolor images were slightly higher than those for DPRIs. ROI1 was found to be significantly lower than ROI2 (P < .001), whereas no difference was found between ROI3 and ROI4 (P = .877). For both observers, the sensitivity and specificity obtained from JBS pseudocolor were above 89%.

CONCLUSION

JBS pseudocolor images can be used for caries detection and offer high sensitivity and specificity.

DentaSeal: A school-based dental sealant efficiency assessment tool to support statewide monitoring and reporting: A field report

BACKGROUND

The evidence base supports effectiveness of dental sealants for prevention of childhood caries in school-aged children.

OBJECTIVE

This study describes planning, development, usability testing and outcomes following implementation of DentaSeal, a web-based application designed to accurately track unique student data and generate reports for all Wisconsin school-based sealant placement (SP) programs.

METHODS

Application software development was informed by a steering committee of representative stakeholders who were interviewed to inform design and provide feedback for design of DentaSeal during development and evaluation. Software development proceeded based on wireframes developed to build architectural design. Usability testing followed and informed any required adjustments to the application. The DentaSeal prototype was beta tested and fully implemented subsequently in the public health sector.

RESULTS

The DentaSeal application demonstrated capacity to: 1) track unique student SP data and longitudinal encounter history, 2) generate reports and 3) support administrative tracking. In 2019, DentaSeal captured SP data of 47 school-based programs in Wisconsin that sponsored > 7,000 program visits for 184,000 children from 62 counties. Delivery of > 548,000 SP services were catalogued.

CONCLUSIONS

For public health initiatives targeting reduction in caries incidence, web-based applications such as DentaSeal represent useful longitudinal tracking tools for cataloguing SP in school-based program participants.

Validating Human-Operant Software: A Case Example

Human-operant experiments conducted with computer software facilitate translational research by assessing the generality of basic research findings and exploring previously untested predictions about behavior in a cost-effective and efficient manner. However, previous human-operant research with computer-based tasks has included little or no description of rigorous validation procedures for the experimental apparatus (i.e., the software used in the experiment). This omission, combined with a general lack of guidance regarding how to thoroughly validate experimental software, introduces the possibility that nascent researchers may insufficiently validate their computer-based apparatus. In this paper, we provide a case example to demonstrate the rigor required to validate experimental software by describing the procedures we used to validate the apparatus reported by Smith and Greer (2021) to assess relapse via a crowdsourcing platform. The validation procedures identified several issues with early iterations of the software, demonstrating how failing to validate human-operant software can introduce confounds into similar experiments. We describe our validation procedures in detail so that others exploring similar computer-based research may have an exemplar for the rigorous testing needed to validate computer software to ensure precision and reliability in computer-based, human-operant experiments.

Osteotomy training for dental students using three-dimensional simulation software and maxillofacial three-dimensional-printed models

PURPOSE/OBJECTIVES

Simulated educational models of teeth, bones, and gums have been used for a long time in procedural skills training in dentistry.  The advent of three-dimensional (3D) printing technologies and additive manufacturing has facilitated the production of more advanced 3D printed models that can be utilized for surgical and dental training together with other technologies (e.g., 3D scanners and image analysis software).

METHODS

We conducted training on osteotomy in the maxilla and mandible using maxillofacial simulation software (MSS) and a 3D-printed model for 5th-year undergraduate dental students (13 students in 2017 and 11 students in 2018 with more than half of their results). We compared the group (13 students) who performed osteotomy after participating in the simulation lecture with those (11 students) who performed osteotomy after performing self-simulation (they were instructed to bring their personal computers and install the MSS) using tests and questionnaires (pre- and post-curriculum).

RESULTS

The average test score was significantly higher in the group who performed osteotomy using the 3D-printed model after performing self-simulation; participants in this group had acquired a better understanding of the surgical procedure. Comparison using questionnaires showed a significant difference in the students' understanding of instruments and surgical techniques between both groups.

CONCLUSION

The MSS and 3D printed models are widely used clinically. Incorporating these in the curriculum will help accelerate student development. In addition, prompt education on the purpose and usefulness of these tools will not only facilitate simulation software and 3D-printed model-based treatment plan in the clinic but also promote further research.

Use of an Open-Source Software to Examine Low Skeletal Muscle Mass in Penile Cancer Patients: A Cross-Sectional Study

Purpose

Low skeletal muscle mass determined radiographically has emerged as an important prognostic marker in penile cancer patients but may be unrecognized in obese patients with a high comorbid disease burden. Moreover, publicly available software for image segmentation are limited. Thus, we describe the prevalence of radiographically low skeletal muscle mass in an obese penile cancer cohort, using an open-source software and examine its association with comorbid disease burden.

Methods

This is a cross-sectional study, utilizing retrospective data from patients diagnosed with penile squamous cell carcinoma between October 2009 and December 2019. Available digital files of perioperative computerized tomography were analyzed, using CoreSlicer, an open-source image segmentation software. The correlation between radiographically low skeletal muscle mass, defined as a skeletal muscle index (SMI) less than 55 cm2/m2 and a Charlson Comorbidity Index (CCI) greater than 4 was examined, using logistic and linear regression.

Results

Forty two of 59 patients had available digital files. Median SMI and body mass index (BMI) were 54.6cm2/m2 and 30.2kg/m2 respectively for the entire cohort. Of included patients, 54% had radiographically low skeletal muscle mass and a median BMI of 28.9 kg/m2. Radiographically low skeletal muscle mass was associated with a CCI greater than 4 on univariable and multivariable logistic regression with odds ratios of 4.85 (p = 0.041) and 7.32 (p = 0.033), respectively. When CCI was treated as a continuous variable on linear regression, the association between radiographically low skeletal muscle mass and CCI was positive, but not statistically significant with an estimated effect of 1.29 (p = 0.1) and 1.27 (p = 0.152) on univariable and multivariable analysis, respectively.

Conclusion

Our data demonstrate that low skeletal muscle mass can be readily assessed with CoreSlicer and is associated with a CCI greater than 4 in obese penile cancer patients.

Comparison of Assessment by a Virtual Patient and by Clinician-Educators of Medical Students' History-Taking Skills: Exploratory Descriptive Study

BACKGROUND

A virtual patient (VP) can be a useful tool to foster the development of medical history-taking skills without the inherent constraints of the bedside setting. Although VPs hold the promise of contributing to the development of students' skills, documenting and assessing skills acquired through a VP is a challenge.

OBJECTIVE

We propose a framework for the automated assessment of medical history taking within a VP software and then test this framework by comparing VP scores with the judgment of 10 clinician-educators (CEs).

METHODS

We built upon 4 domains of medical history taking to be assessed (breadth, depth, logical sequence, and interviewing technique), adapting these to be implemented into a specific VP environment. A total of 10 CEs watched the screen recordings of 3 students to assess their performance first globally and then for each of the 4 domains.

RESULTS

The scores provided by the VPs were slightly higher but comparable with those given by the CEs for global performance and for depth, logical sequence, and interviewing technique. For breadth, the VP scores were higher for 2 of the 3 students compared with the CE scores.

CONCLUSIONS

Findings suggest that the VP assessment gives results akin to those that would be generated by CEs. Developing a model for what constitutes good history-taking performance in specific contexts may provide insights into how CEs generally think about assessment.

Computing and Oral Health: Mobile Solution for Collecting, Data Analysis, Managing and Reproducing Epidemiological Research in Population Groups

Epidemiological inquiries study and evaluate the health status of the population. For dental caries, the World Health Organization (WHO) recommends the DMFT and DMFS indexes, which represent the sum of the decayed, missing and filled teeth, divided by the population studied. Traditionally these surveys are conducted using cellulose paper sheet. This study describes the development and presents the field performance of NutriOdonto, a software created for an Oral Health Survey carried out in 2018 and 2019 involving 2578 students from the municipal schools of Palmas/TO, located in the Brazilian Amazon region. This is a descriptive, applied research on the development of a software for the collecting, analysis, management and reproducibility of oral health epidemiological research. A software applied to the collecting, analysis and formation of the database was developed through the information obtained from the questionnaires applied to the participants of the study and the completion of the electronic oral examination form. Recent Information and Communication Technologies (ICT) are intelligently configured to create models and mobile applications (Apps) that can be useful to manage health issues, thus broadening the perspective of service provision in this sector. Some of these mobile devices, tablets and smartphones are being developed to generate information, for collection, recording, storage and analysis of oral health epidemiological research data. NutriOdonto contributed to the rapid collection, recording and storage of information, in the construction of the database and its analysis. Replacing paper forms with electronic forms minimized possible typos, reduced the use of cellulose paper and the financial costs, among other things. This software can contribute to decision making by managers and professionals and to improving the planning and implementation of actions in health promotion and oral disease prevention.

The Internet-Based Cognitive Assessment Tool: System Design and Feasibility Study

BACKGROUND

Persistent cognitive impairment is prevalent in unipolar and bipolar disorders and is associated with decreased quality of life and psychosocial dysfunction. The screen for cognitive impairment in psychiatry (SCIP) test is a validated paper-and-pencil instrument for the assessment of cognition in affective disorders. However, there is no digital cognitive screening tool for the brief and accurate assessment of cognitive impairments in this patient group.

OBJECTIVE

In this paper, we present the design process and feasibility study of the internet-based cognitive assessment tool (ICAT) that is designed based on the cognitive tasks of the SCIP. The aims of this feasibility study were to perform the following tasks among healthy individuals: (1) evaluate the usability of the ICAT, (2) investigate the feasibility of the ICAT as a patient-administered cognitive assessment tool, and (3) examine the performance of automatic speech recognition (ASR) for the assessment of verbal recall.

METHODS

The ICAT was developed in a user-centered design process. The cognitive measures of the ICAT were immediate and delayed recall, working memory, and psychomotor speed. Usability and feasibility studies were conducted separately with 2 groups of healthy individuals (N=21 and N=19, respectively). ICAT tests were available in the English and Danish languages. The participants were asked to fill in the post study system usability questionnaire (PSSUQ) upon completing the ICAT test. Verbal recall in the ICAT was assessed using ASR, and the performance evaluation criterion was word error rate (WER). A Pearson 2-tailed correlation analysis significant at the .05 level was applied to investigate the association between the SCIP and ICAT scores.

RESULTS

The overall psychometric factors of PSSUQ for both studies gave scores above 4 (out of 5). The analysis of the feasibility study revealed a moderate to strong correlation between the total scores of the SCIP and ICAT (r=0.63; P=.009). There were also moderate to strong correlations between the SCIP and ICAT subtests for immediate verbal recall (r=0.67; P=.002) and psychomotor speed (r=0.71; P=.001). The associations between the respective subtests for working memory, executive function, and delayed recall, however, were not statistically significant. The corresponding WER for English and Danish responses were 17.8% and 6.3%, respectively.

CONCLUSIONS

The ICAT is the first digital screening instrument modified from the SCIP using Web-based technology and ASR. There was good accuracy of the ASR for verbal memory assessment. The moderate correlation between the ICAT and SCIP scores suggests that the ICAT is a valid tool for assessing cognition, although this should be confirmed in a larger study with greater statistical power. Taken together, the ICAT seems to be a valid Web-based cognitive assessment tool that, after some minor modifications and further validation, may be used to screen for cognitive impairment in clinical settings.

Web-based application for threatened woodland caribou population modeling

Woodland caribou (Rangifer tarandus caribou) are threatened in Canada, with population and distribution declines evident in most regions of the country. Causes of declines are linked to landscape change from forest fires and human development, notably forestry oil and gas activities, which result in caribou habitat loss and affect ecosystem food webs. The Federal Species at Risk Act requires effective protection and restoration of caribou habitat, with actions to increase caribou survival. These requirements call for effective monitoring of caribou population trends to gauge success. Many woodland caribou populations are nearly impossible to count using traditional aerial survey methods, but demographic‐based monitoring approaches can be used to estimate population trends based on population modeling of vital rates from marked animals. Monitoring programs have used a well‐known simple population model (the Recruitment‐Mortality [R/M] equation) to estimate demographic rates for woodland caribou, but have faced challenges in managing large data streams and providing transparency in the demographic estimation process. We present a stand‐alone statistical software application using open‐source software to permit efficient, transparent, and replicable demographic estimation for woodland caribou populations. We developed an easy‐to‐use, interactive web‐based application for the R/M population model that uses a Bayesian estimation approach and provides the user flexibility in choice of prior distributions and other output features. We illustrate the web‐application to the A la Pêche Southern Mountain (Central Group) woodland caribou population in west‐central Alberta, Canada, during 1998–2017. Our estimates of population demographics are consistent with previous research on this population and highlight the utility of the application in assessing caribou population responses to species recovery actions. We provide example data, computer code, the web‐based application package, and a user manual to guide installation and use. We also review underlying assumptions and challenges of population monitoring in this case study. We expect our software will contribute to efficient monitoring of woodland caribou and help in the assessment of recovery actions for this species. © 2019 The Authors. Wildlife Society Bulletin Published by Wiley Periodicals, Inc.

We developed a stand‐alone Web‐Application to support population trend estimation for endangered and threatened woodland caribou populations.

System for Quality-Assured Data Analysis: Flexible, reproducible scientific workflows

The reproducibility of scientific processes is one of the paramount problems of bioinformatics, an engineering problem that must be addressed to perform good research. The System for Quality-Assured Data Analysis (SyQADA), described here, seeks to address reproducibility by managing many of the details of procedural bookkeeping in bioinformatics in as simple and transparent a manner as possible. SyQADA has been used by persons with backgrounds ranging from expert programmer to Unix novice, to perform and repeat dozens of diverse bioinformatics workflows on tens of thousands of samples, consuming over 80 CPU-months of computing on over 300,000 individual tasks of scores of projects on laptops, computer servers, and computing clusters. SyQADA is especially well-suited for paired-sample analyses found in cancer tumor-normal studies. SyQADA executable source code, documentation, tutorial examples, and workflows used in our lab is available from http://scheet.org/software.html.

APS Data Management System

As the capabilities of modern X-ray detectors and acquisition technologies increase, so do the data rates and volumes produced at synchrotron beamlines. This brings into focus a number of challenges related to managing data at such facilities, including data transfer, near real-time data processing, automated processing pipelines, data storage, handling metadata and remote user access to data. The Advanced Photon Source Data Management System software is designed to help beamlines deal with these issues. This paper presents the system architecture and describes its components and functionality; the system's current usage is discussed, examples of its use have been provided and future development plans are outlined.

First online real-time evaluation of motion-induced 4D dose errors during radiotherapy delivery

PURPOSE

In radiotherapy, dose deficits caused by tumor motion often far outweigh the discrepancies typically allowed in plan-specific quality assurance (QA). Yet, tumor motion is not usually included in present QA. We here present a novel method for online treatment verification by real-time motion-including four-dimensional (4D) dose reconstruction and dose evaluation and demonstrate its use during stereotactic body radiotherapy (SBRT) delivery with and without MLC tracking.

METHODS

Five volumetric-modulated arc therapy (VMAT) plans were delivered with and without MLC tracking to a motion stage carrying a Delta4 dosimeter. The VMAT plans have previously been used for (nontracking) liver SBRT with intratreatment tumor motion recorded by kilovoltage intrafraction monitoring (KIM). The motion stage reproduced the KIM-measured tumor motions in three dimensions (3D) while optical monitoring guided the MLC tracking. Linac parameters and the target position were streamed to an in-house developed software program (DoseTracker) that performed real-time 4D dose reconstructions and 3%/3 mm γ-evaluations of the reconstructed cumulative dose using a concurrently reconstructed planned dose without target motion as reference. Offline, the real-time reconstructed doses and γ-evaluations were validated against 4D dosimeter measurements performed during the experiments.

RESULTS

In total, 181,120 dose reconstructions and 5,237 γ-evaluations were performed online and in real time with median computation times of 30 ms and 1.2 s, respectively. The mean (standard deviation) difference between reconstructed and measured doses was -1.2% (4.9%) for transient doses and -1.5% (3.9%) for cumulative doses. The root-mean-square deviation between reconstructed and measured motion-induced γ-fail rates was 2.0%-point. The mean (standard deviation) sensitivity and specificity of DoseTracker to predict γ-fail rates above a given threshold was 96.8% (3.5%) and 99.2% (0.4%), respectively, for clinically relevant thresholds between 1% and 30% γ-fail rate.

CONCLUSIONS

Real-time delivery-specific QA during radiotherapy of moving targets was demonstrated for the first time. It allows supervision of treatment accuracy and action on treatment discrepancy within 2 s with high sensitivity and specificity.

Comparative analysis of respiratory motion tracking using Microsoft Kinect v2 sensor

PURPOSE

To present and evaluate a straightforward implementation of a marker-less, respiratory motion-tracking process utilizing Kinect v2 camera as a gating tool during 4DCT or during radiotherapy treatments.

METHODS

Utilizing the depth sensor on the Kinect as well as author written C# code, respiratory motion of a subject was tracked by recording depth values obtained at user selected points on the subject, with each point representing one pixel on the depth image. As a patient breathes, specific anatomical points on the chest/abdomen will move slightly within the depth image across pixels. By tracking how depth values change for a specific pixel, instead of how the anatomical point moves throughout the image, a respiratory trace can be obtained based on changing depth values of the selected pixel. Tracking these values was implemented via marker-less setup. Varian's RPM system and the Anzai belt system were used in tandem with the Kinect to compare respiratory traces obtained by each using two different subjects.

RESULTS

Analysis of the depth information from the Kinect for purposes of phase- and amplitude-based binning correlated well with the RPM and Anzai systems. Interquartile Range (IQR) values were obtained comparing times correlated with specific amplitude and phase percentages against each product. The IQR time spans indicated the Kinect would measure specific percentage values within 0.077 s for Subject 1 and 0.164 s for Subject 2 when compared to values obtained with RPM or Anzai. For 4DCT scans, these times correlate to less than 1 mm of couch movement and would create an offset of 1/2 an acquired slice.

CONCLUSION

By tracking depth values of user selected pixels within the depth image, rather than tracking specific anatomical locations, respiratory motion can be tracked and visualized utilizing the Kinect with results comparable to that of the Varian RPM and Anzai belt.

A Natural Language Processing System That Links Medical Terms in Electronic Health Record Notes to Lay Definitions: System Development Using Physician Reviews

Background

Many health care systems now allow patients to access their electronic health record (EHR) notes online through patient portals. Medical jargon in EHR notes can confuse patients, which may interfere with potential benefits of patient access to EHR notes.

Objective

The aim of this study was to develop and evaluate the usability and content quality of NoteAid, a Web-based natural language processing system that links medical terms in EHR notes to lay definitions, that is, definitions easily understood by lay people.

Methods

NoteAid incorporates two core components: CoDeMed, a lexical resource of lay definitions for medical terms, and MedLink, a computational unit that links medical terms to lay definitions. We developed innovative computational methods, including an adapted distant supervision algorithm to prioritize medical terms important for EHR comprehension to facilitate the effort of building CoDeMed. Ten physician domain experts evaluated the user interface and content quality of NoteAid. The evaluation protocol included a cognitive walkthrough session and a postsession questionnaire. Physician feedback sessions were audio-recorded. We used standard content analysis methods to analyze qualitative data from these sessions.

Results

Physician feedback was mixed. Positive feedback on NoteAid included (1) Easy to use, (2) Good visual display, (3) Satisfactory system speed, and (4) Adequate lay definitions. Opportunities for improvement arising from evaluation sessions and feedback included (1) improving the display of definitions for partially matched terms, (2) including more medical terms in CoDeMed, (3) improving the handling of terms whose definitions vary depending on different contexts, and (4) standardizing the scope of definitions for medicines. On the basis of these results, we have improved NoteAid’s user interface and a number of definitions, and added 4502 more definitions in CoDeMed.

Conclusions

Physician evaluation yielded useful feedback for content validation and refinement of this innovative tool that has the potential to improve patient EHR comprehension and experience using patient portals. Future ongoing work will develop algorithms to handle ambiguous medical terms and test and evaluate NoteAid with patients.

Virtual protein purification: A simple exercise to introduce ph as a parameter that effects ion exchange chromatography

This article describes a simple exercise using a free, easy-to-use, established online program. The exercise helps to reinforce protein purification concepts and introduces undergraduates to pH as a parameter that affects anion-exchange chromatography. The exercise was tested with biochemistry majors at California State University-Chico. Given the versatility of the program, this work is also a model for instructors that wish to develop their own exercise to help teach other protein purification techniques. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):91-97, 2018.

A Novel Computer-Based Set-Up to Study Movement Coordination in Human Ensembles

Existing experimental works on movement coordination in human ensembles mostly investigate situations where each subject is connected to all the others through direct visual and auditory coupling, so that unavoidable social interaction affects their coordination level. Here, we present a novel computer-based set-up to study movement coordination in human groups so as to minimize the influence of social interaction among participants and implement different visual pairings between them. In so doing, players can only take into consideration the motion of a designated subset of the others. This allows the evaluation of the exclusive effects on coordination of the structure of interconnections among the players in the group and their own dynamics. In addition, our set-up enables the deployment of virtual computer players to investigate dyadic interaction between a human and a virtual agent, as well as group synchronization in mixed teams of human and virtual agents. We show how this novel set-up can be employed to study coordination both in dyads and in groups over different structures of interconnections, in the presence as well as in the absence of virtual agents acting as followers or leaders. Finally, in order to illustrate the capabilities of the architecture, we describe some preliminary results. The platform is available to any researcher who wishes to unfold the mechanisms underlying group synchronization in human ensembles and shed light on its socio-psychological aspects.

Consistency mapping of 16 lymph node stations in gastric cancer by CT-based vessel-guided delineation of 255 patients

In order to refine the location and metastasis-risk density of 16 lymph node stations of gastric cancer for neoadjuvant radiotherapy, we retrospectively reviewed the initial images and pathological reports of 255 gastric cancer patients with lymphatic metastasis. Metastatic lymph nodes identified in the initial computed tomography images were investigated by two radiologists with gastrointestinal specialty. A circle with a diameter of 5 mm was used to identify the central position of each metastatic lymph node, defined as the LNc (the central position of the lymph node). The LNc was drawn at the equivalent location on the reference images of a standard patient based on the relative distances to the same reference vessels and the gastric wall using a Monaco® version 5.0 workstation. The image manipulation software Medi-capture was programmed for image analysis to produce a contour and density atlas of 16 lymph node stations. Based on a total of 2846 LNcs contoured (31-599 per lymph node station), we created a density distribution map of 16 lymph node drainage stations of the stomach on computed tomography images, showing the detailed radiographic delineation of each lymph node station as well as high-risk areas for lymph node metastasis. Our mapping can serve as a template for the delineation of gastric lymph node stations when defining clinical target volume in pre-operative radiotherapy for gastric cancer.

Age estimation by dentin translucency measurement using digital method: An institutional study

Aims:

The aims of the present study were to measure translucency on sectioned teeth using available computer hardware and software, to correlate dimensions of root dentin translucency with age, and to assess whether translucency is reliable for age estimation.

Materials and Methods:

A pilot study was done on 62 freshly extracted single-rooted permanent teeth from 62 different individuals (35 males and 27 females) and their 250 μm thick sections were prepared by micromotor, carborundum disks, and Arkansas stone. Each tooth section was scanned and the images were opened in the Adobe Photoshop software. Measurement of root dentin translucency (TD length) was done on the scanned image by placing two guides (A and B) along the x-axis of ABFO NO. 2 scale. Unpaired t-test, regression analysis, and Pearson correlation coefficient were used as statistical tools.

Results:

A linear relationship was observed between TD length and age in the regression analysis. The Pearson correlation analysis showed that there was positive correlation (r = 0.52, P = 0.0001) between TD length and age. However, no significant (P > 0.05) difference was observed in the TD length between male (8.44 ± 2.92 mm) and female (7.80 ± 2.79 mm) samples.

Conclusion:

Translucency of the root dentin increases with age and it can be used as a reliable parameter for the age estimation. The method used here to digitally select and measure translucent root dentin is more refined, better correlated to age, and produce superior age estimation.

A Novel Computer-Based Set-Up to Study Movement Coordination in Human Ensembles

Existing experimental works on movement coordination in human ensembles mostly investigate situations where each subject is connected to all the others through direct visual and auditory coupling, so that unavoidable social interaction affects their coordination level. Here, we present a novel computer-based set-up to study movement coordination in human groups so as to minimize the influence of social interaction among participants and implement different visual pairings between them. In so doing, players can only take into consideration the motion of a designated subset of the others. This allows the evaluation of the exclusive effects on coordination of the structure of interconnections among the players in the group and their own dynamics. In addition, our set-up enables the deployment of virtual computer players to investigate dyadic interaction between a human and a virtual agent, as well as group synchronization in mixed teams of human and virtual agents. We show how this novel set-up can be employed to study coordination both in dyads and in groups over different structures of interconnections, in the presence as well as in the absence of virtual agents acting as followers or leaders. Finally, in order to illustrate the capabilities of the architecture, we describe some preliminary results. The platform is available to any researcher who wishes to unfold the mechanisms underlying group synchronization in human ensembles and shed light on its socio-psychological aspects.

Real-time 4D dose reconstruction for tracked dynamic MLC deliveries for lung SBRT

PURPOSE

This study provides a proof of concept for real-time 4D dose reconstruction for lung stereotactic body radiation therapy (SBRT) with multileaf collimator (MLC) tracking and assesses the impact of tumor tracking on the size of target margins.

METHODS

The authors have implemented real-time 4D dose reconstruction by connecting their tracking and delivery software to an Agility MLC at an Elekta Synergy linac and to their in-house treatment planning software (TPS). Actual MLC apertures and (simulated) target positions are reported to the TPS every 40 ms. The dose is calculated in real-time from 4DCT data directly after each reported aperture by utilization of precalculated dose-influence data based on a Monte Carlo algorithm. The dose is accumulated onto the peak-exhale (reference) phase using energy-mass transfer mapping. To investigate the impact of a potentially reducible safety margin, the authors have created and delivered treatment plans designed for a conventional internal target volume (ITV) + 5 mm, a midventilation approach, and three tracking scenarios for four lung SBRT patients. For the tracking plans, a moving target volume (MTV) was established by delineating the gross target volume (GTV) on every 4DCT phase. These were rigidly aligned to the reference phase, resulting in a unified maximum GTV to which a 1, 3, or 5 mm isotropic margin was added. All scenarios were planned for 9-beam step-and-shoot IMRT to meet the criteria of RTOG 1021 (3 × 18 Gy). The GTV 3D center-of-volume shift varied from 6 to 14 mm.

RESULTS

Real-time dose reconstruction at 25 Hz could be realized on a single workstation due to the highly efficient implementation of dose calculation and dose accumulation. Decreased PTV margins resulted in inadequate target coverage during untracked deliveries for patients with substantial tumor motion. MLC tracking could ensure the GTV target dose for these patients. Organ-at-risk (OAR) doses were consistently reduced by decreased PTV margins. The tracked MTV + 1 mm deliveries resulted in the following OAR dose reductions: lung V20 up to 3.5%, spinal cord D2 up to 0.9 Gy/Fx, and proximal airways D2 up to 1.4 Gy/Fx.

CONCLUSIONS

The authors could show that for patient data at clinical resolution and realistic motion conditions, the delivered dose could be reconstructed in 4D for the whole lung volume in real-time. The dose distributions show that reduced margins yield lower doses to healthy tissue, whilst target dose can be maintained using dynamic MLC tracking.

Automated Glycan Sequencing from Tandem Mass Spectra of N-Linked Glycopeptides

Mass spectrometry has become a routine experimental tool for proteomic biomarker analysis of human blood samples, partly due to the large availability of informatics tools. As one of the most common protein post-translational modifications (PTMs) in mammals, protein glycosylation has been observed to alter in multiple human diseases and thus may potentially be candidate markers of disease progression. While mass spectrometry instrumentation has seen advancements in capabilities, discovering glycosylation-related markers using existing software is currently not straightforward. Complete characterization of protein glycosylation requires the identification of intact glycopeptides in samples, including identification of the modification site as well as the structure of the attached glycans. In this paper, we present GlycoSeq, an open-source software tool that implements a heuristic iterated glycan sequencing algorithm coupled with prior knowledge for automated elucidation of the glycan structure within a glycopeptide from its collision-induced dissociation tandem mass spectrum. GlycoSeq employs rules of glycosidic linkage as defined by glycan synthetic pathways to eliminate improbable glycan structures and build reasonable glycan trees. We tested the tool on two sets of tandem mass spectra of N-linked glycopeptides cell lines acquired from breast cancer patients. After employing enzymatic specificity within the N-linked glycan synthetic pathway, the sequencing results of GlycoSeq were highly consistent with the manually curated glycan structures. Hence, GlycoSeq is ready to be used for the characterization of glycan structures in glycopeptides from MS/MS analysis. GlycoSeq is released as open source software at https://github.com/chpaul/GlycoSeq/ .

Choosing the best image processing method for masticatory performance assessment when using two-coloured specimens

Objective masticatory performance assessment using two-coloured specimens relies on image processing techniques; however, just a few approaches have been tested and no comparative studies are reported. The aim of this study was to present a selection procedure of the optimal image analysis method for masticatory performance assessment with a given two-coloured chewing gum. Dentate participants (n = 250; 25 ± 6·3 years) chewed red-white chewing gums for 3, 6, 9, 12, 15, 18, 21 and 25 cycles (2000 samples). Digitalised images of retrieved specimens were analysed using 122 image processing methods (IPMs) based on feature extraction algorithms (pixel values and histogram analysis). All IPMs were tested following the criteria of: normality of measurements (Kolmogorov-Smirnov), ability to detect differences among mixing states (anova corrected with post hoc Bonferroni) and moderate-to-high correlation with the number of cycles (Spearman's Rho). The optimal IPM was chosen using multiple criteria decision analysis (MCDA). Measurements provided by all IPMs proved to be normally distributed (P < 0·05), 116 proved sensible to mixing states (P < 0·05), and 35 showed moderate-to-high correlation with the number of cycles (|ρ| > 0·5; P < 0·05). The variance of the histogram of the Hue showed the highest correlation with the number of cycles (ρ = 0·792; P < 0·0001) and the highest MCDA score (optimal). The proposed procedure proved to be reliable and able to select the optimal approach among multiple IPMs. This experiment may be reproduced to identify the optimal approach for each case of locally available test foods.

Conventional versus digital approach for measuring dentin translucency in forensic age estimation

BACKGROUND

Root dentine translucency remains the method of choice providing the most accurate results for age estimation. Conventionally, translucency is measured using calipers. In recent times, computer-based methods are proposed, which require the use of custom-built software programs.

AIMS AND OBJECTIVES

The aim was to use a digital method to measure dentinal translucency on sectioned teeth and to compare digital measurements to conventionally obtained translucency measurements.

MATERIALS AND METHODS

A total of 200 extracted permanent teeth were collected and were sectioned to a thickness of 250 μm. Translucency measurements were obtained using the digital method and compared with those obtained using a caliper.

RESULTS

Correlation coefficients of translucency measurements to age were statistically significant for both methods (P < 0.001), although marginally higher correlation was observed for the conventional method (r = 0.612). Application of derived linear regression equations on an independent sample (n = 25) suggested that conventional approach is marginally better in estimating age to within 5 years of the actual age, both the methods are similar in assessing age within 5-10 years of the actual age, and digital approach is marginally better in estimating age beyond 10 years of actual age.

CONCLUSION

The translucency measurements obtained by the two methods were identical, with no clear superiority of one method over the other.

Effect of nitrate on nodule and root growth of soybean (Glycine max (L.) Merr.)

The application of combined nitrogen, especially nitrate, to soybean plants is known to strongly inhibit nodule formation, growth and nitrogen fixation. In the present study, we measured the effects of supplying 5 mM nitrate on the growth of nodules, primary root, and lateral roots under light at 28 °C or dark at 18 °C conditions. Photographs of the nodulated roots were periodically taken by a digital camera at 1-h intervals, and the size of the nodules was measured with newly developed computer software. Nodule growth was depressed approximately 7 h after the addition of nitrate under light conditions. The nodule growth rate under dark conditions was almost half that under light conditions, and nodule growth was further suppressed by the addition of 5 mM nitrate. Similar results were observed for the extending growth rate of the primary root as those for nodule growth supplied with 5 mM nitrate under light/dark conditions. In contrast, the growth of lateral roots was promoted by the addition of 5 mM nitrate. The 2D-PAGE profiles of nodule protein showed similar patterns between the 0 and 5 mM nitrate treatments, which suggested that metabolic integrity may be maintained with the 5 mM nitrate treatment. Further studies are required to confirm whether light or temperature condition may give the primary effect on the growth of nodules and roots.

Digital approach for measuring dentin translucency in forensic age estimation

Background:

Dentin translucency is best suited for age estimation not only in terms of accuracy but also in terms of simplicity. Conventionally, translucency has been measured using calipers. Computer-based methods have been proposed for the same, although these required the use of custom-built software programs.

Objectives:

The objectives of the study were to use a simple digital method to measure dentinal translucency on sectioned teeth and to compare digital measurements to conventionally obtained translucency measurements.

Materials and Methods:

Fifty extracted permanent teeth were collected and were sectioned to 250 μm. Translucency measurements were obtained using the digital method and compared with those obtained using a caliper.

Results:

Correlation coefficients of translucency measurements to age were statistically significant for both methods (P < 0.001), and marginally higher for the conventional approach (r = 0.4671). Application of derived linear regression equations on an independent sample (n = 10) revealed a similar ability of both the methods to assess age to within ±5 years of the actual age.

Conclusion:

The translucency measurements obtained by the two methods were very similar, with no clear superiority of one method over the other. Hence, further studies on a large scale are warranted to determine which method is more reliable to estimate the age.

Recent advances in the structure elucidation of small organic molecules by the LSD software

The LSD software proposes the structures of small organic molecules that fit with structural constraints from 1D and 2D NMR spectroscopy. Its initial design introduced limits that needed to be eliminated to extend its scope and help its users choose the most likely structure among those proposed. The LSD software code has been improved, so that it recognizes a wider set of atom types to build molecules. More flexibility has been given in the interpretation of 2D NMR data, including the automatic detection of very long-range correlations. A program named pyLSD was written to deal with problems in which atom types are ambiguously defined. It also provides a (13)C NMR chemical shift-based solution ranking algorithm. PyLSD was able to propose the correct structure of hexacyclinol, a natural product whose structure determination has been highly controversal. The solution was ranked first within a list of ten structures that were produced by pyLSD from the literature NMR data. The structure of an aporphin natural product was determined by pyLSD, taking advantage of the possibility of handling electrically charged atoms. The structure generation of the insect antifeedant azadirachtin by LSD was reinvestigated by pyLSD, considering that three (13)C resonances did not lead to univocal hybridization states.

Technology-based dietary assessment: development of the Synchronised Nutrition and Activity Program (SNAP)

BACKGROUND

Accurate, reliable and feasible methods of dietary intake and physical activity assessment are required to improve our understanding of the associations between energy balance-related behaviours and health.

METHODS

The Synchronised Nutrition and Activity Program (SNAP) was developed to enhance recall in children by integrating new and established methods of dietary intake and physical activity recall. A list of commonly consumed foods (n = 40), drinks (n = 9) and physical activities (n = 29) was used in SNAP. All foods and drinks were analysed by count (i.e., the number of times a particular food was selected), as a proxy indicator of dietary behaviours. All reported physical activities were assigned an intensity code [in metabolic equivalents (METs)] to determine minutes of moderate-vigorous activity (MVPA; ≥3 METs).

RESULTS

Most participants completed a whole day's recall (both dietary intake and physical activities) in less than 25 min. SNAP was compared against 24-h multiple pass questionnaire and accelerometry in 121 children (aged 7-15 years old). For dietary variables, the accuracy of SNAP(™) (mean difference) was within ±1 count for the majority of food groups. The proportion of the sample with a between-method agreement within ±1 count ranged from 0.40 to 0.99. For MVPA, there was no substantial fixed or proportional bias, with a mean difference between methods (SNAP) - accelerometry) of -9 min of MVPA. Qualitatively, participants have indicated that they find SNAP easy and fun to use.

CONCLUSIONS

SNAP was developed to be a simple, quick and engaging method of assessing energy balance-related behaviours at a group or population level and succeeded because it can collect a whole day's recall (dietary intake and physical activities) in less than 25 min to a reasonable and acceptable degree of accuracy.

Preformed vs intraoperative bending of titanium mesh for orbital reconstruction

OBJECTIVE

The most accurate orbital reconstructions result from an anatomic repair of the premorbid orbital architecture. Many different techniques and materials have been used; unfortunately, there is currently no optimal method. This study compares the use of preformed vs intraoperative bending of titanium mesh for orbital reconstruction in 2-wall orbital fractures.

STUDY DESIGN

Cadaver-based study.

SETTING

University hospital.

SUBJECTS AND METHODS

Preinjury computed tomography scans were obtained in 15 cadaveric heads (30 orbits). Stereolithographic (STL) models were fabricated for 5 of the specimens (10 orbits). Two wall fractures (lamina papyracea and floor) were then generated in all orbits. Surgical reconstruction was performed in all orbits using 1 of 3 techniques (10 orbits each): (1) patient-specific implant molded from the preinjury STL model, (2) titanium mesh sheet bent freehand, and (3) preformed titanium mesh. Each technique was evaluated for orbital volume correction, contour accuracy, ease of use, and cost.

RESULTS

No difference in volume restoration was found between the 3 techniques. Patient-specific implants had the greatest contour accuracy, poor ease of use, and highest cost. Freehand bending implants had the poorest contour accuracy, acceptable ease of use, and lowest cost. Preformed mesh implants had intermediate contour accuracy, excellent ease of use, and low cost.

CONCLUSION

All 3 techniques provide equivalent orbital volume correction. However, preformed mesh implants have many advantages based on contour accuracy, ease of use, and relative cost.

A microsoft excel(®) 2010 based tool for calculating interobserver agreement

This technical report provides detailed information on the rationale for using a common computer spreadsheet program (Microsoft Excel(®)) to calculate various forms of interobserver agreement for both continuous and discontinuous data sets. In addition, we provide a brief tutorial on how to use an Excel spreadsheet to automatically compute traditional total count, partial agreement-within-intervals, exact agreement, trial-by-trial, interval-by-interval, scored-interval, unscored-interval, total duration, and mean duration-per-interval interobserver agreement algorithms. We conclude with a discussion of how practitioners may integrate this tool into their clinical work.

Automated dose-rounding recommendations for pediatric medications

BACKGROUND

Although pediatric electronic prescribing systems are increasingly being used in pediatric care, many of these systems lack the clinical decision-support infrastructure needed to calculate a safe and effective rounded medication dose. This infrastructure is required to facilitate tailoring of established dosing guidance while maintaining the medication's therapeutic intent.

OBJECTIVE

The goal of this project was to establish best practices for generating an appropriate medication dose and to create an interoperable rounding knowledge base combining best practices and dose-rounding information.

METHODS

We interviewed 19 pediatric health care and pediatric pharmacy experts and conducted a literature review. After using these data to construct initial rounding tolerances, we used a Delphi process to achieve consensus about the rounding tolerance for each commonly prescribed medication.

RESULTS

Three categories for medication-rounding philosophy emerged from our literature review: (1) medications for which rounding is used judiciously to retain the intended effect; (2) medications that are rounded with attention to potential unintended effects; and (3) medications that are rarely rounded because of the potential for toxicity. We assigned a small subset of medications to a fourth category-inadequate data-for which there was insufficient information to provide rounding recommendations. For all 102 medications, we were able to arrive at a consensus recommendation for rounding a given calculated dose.

CONCLUSIONS

Results of this study provide the pediatric information technology community with a primary set of recommended rounding tolerances for commonly prescribed drugs. The interoperable knowledge base developed here can be integrated with existing and developing electronic prescribing systems, potentially improving prescribing safety and reducing cognitive workload.

PSEUDOMARKER: a powerful program for joint linkage and/or linkage disequilibrium analysis on mixtures of singletons and related individuals

A decade ago, there was widespread enthusiasm for the prospects of genome-wide association studies to identify common variants related to common chronic diseases using samples of unrelated individuals from populations. Although technological advancements allow us to query more than a million SNPs across the genome at low cost, a disappointingly small fraction of the genetic portion of common disease etiology has been uncovered. This has led to the hypothesis that less frequent variants might be involved, stimulating a renaissance of the traditional approach of seeking genes using multiplex families from less diverse populations. However, by using the modern genotyping and sequencing technology, we can now look not just at linkage, but jointly at linkage and linkage disequilibrium (LD) in such samples. Software methods that can look simultaneously at linkage and LD in a powerful and robust manner have been lacking. Most algorithms cannot jointly analyze datasets involving families of varying structures in a statistically or computationally efficient manner. We have implemented previously proposed statistical algorithms in a user-friendly software package, PSEUDOMARKER. This paper is an announcement of this software package. We describe the motivation behind the approach, the statistical methods, and software, and we briefly demonstrate PSEUDOMARKER's advantages over other packages by example.

Creating single-subject design graphs in Microsoft Excel 2007

Over 10 years have passed since the publication of Carr and Burkholder's (1998) technical article on how to construct single-subject graphs using Microsoft Excel. Over the course of the past decade, the Excel program has undergone a series of revisions that make the Carr and Burkholder paper somewhat difficult to follow with newer versions. The present article provides task analyses for constructing various types of commonly used single-subject design graphs in Microsoft Excel 2007. The task analyses were evaluated using a between-subjects design that compared the graphing skills of 22 behavior-analytic graduate students using Excel 2007 and either the Carr and Burkholder or newly developed task analyses. Results indicate that the new task analyses yielded more accurate and faster graph construction than the Carr and Burkholder instructions.

Implementation of card: curve-fitting allelochemical response data

Bioassay techniques are essential methods used to study the effects of allelochemicals on plant processes. It is often observed that the biological processes are stimulated at low allelochemical concentrations and inhibited as the concentrations increase. Liu et al., (2003) developed a simple model to fit this type of allelochemical response data. Based on the model, CARD (curve-fitting allelochemical response data) was developed as a Windows based program that can be used to fit a stimulation-inhibition response data. An example of using CARD is given.