Ten simple rules for implementing open and reproducible research practices after attending a training course.

Open, reproducible, and replicable research practices are a fundamental part of science. Training is often organized on a grassroots level, offered by early career researchers, for early career researchers. Buffet style courses that cover many topics can inspire participants to try new things; however, they can also be overwhelming. Participants who want to implement new practices may not know where to start once they return to their research team. We describe ten simple rules to guide participants of relevant training courses in implementing robust research practices in their own projects, once they return to their research group. This includes (1) prioritizing and planning which practices to implement, which involves obtaining support and convincing others involved in the research project of the added value of implementing new practices; (2) managing problems that arise during implementation; and (3) making reproducible research and open science practices an integral part of a future research career. We also outline strategies that course organizers can use to prepare participants for implementation and support them during this process.

Children's memory "in the wild": examining the temporal organization of free recall from a week-long camp at a local zoo.

Free-recall paradigms have greatly influenced our understanding of memory. The majority of this research involves laboratory-based events (e.g., word lists) that are studied and tested within minutes. This literature shows that adults recall events in a temporally organized way, with successive responses often coming from neighboring list positions (i.e., temporal clustering) and with enhanced memorability of items from the end of a list (i.e., recency). Temporal clustering effects are so robust that temporal organization is described as a fundamental memory property. Yet relatively little is known about the development of this temporal structure across childhood, and even less about children's memory search for real-world events occurring over an extended period. In the present work, children (N = 144; 3 age groups: 4-5-year-olds, 6-7-year-olds, 8-10-year-olds) took part in a 5-day summer camp at a local zoo. The camp involved various dynamic events, including daily animal exhibit visits. On day 5, children were asked to recall all the animals they visited. We found that overall recall performance, in terms of number of animals recalled, improved steadily across childhood. Temporal organization and recency effects showed different developmental patterns. Temporal clustering was evident in the response sequences for all age groups and became progressively stronger across childhood. In contrast, the recency advantage, when characterized as a proportion of total responses, was stable across age groups. Thus, recall dynamics in early childhood parallel that seen in adulthood, with continued development of temporal organization across middle to late childhood.

Evolving Role of Dual-Energy CT in the Clinical Workup of Gout: A Retrospective Study.

BACKGROUND. Dual-energy CT (DECT) allows noninvasive detection of monosodium urate (MSU) crystal deposits and has become incorporated into the routine clinical evaluation for gout at many institutions over the past decade. OBJECTIVE. The purpose of this study was to compare two time periods over the past decade in terms of radiologists' interpretations of DECT examinations performed for the evaluation of gout and subsequent clinical actions. METHODS. This retrospective study included 100 consecutive adult patients who underwent DECT to evaluate for gout in each of two periods (one beginning in March 2013 and one beginning in September 2019). Examinations performed in 2013 were conducted using a second-generation DECT scanner (80 kV [tube A] and 140 kV [tube B] with a 0.4-mm tin filter), and those performed in 2019 were conducted using a third-generation DECT scanner (80 kV [tube A] and 150 kV [tube B] with a 0.6-mm tin filter) that provides improved spectral separation. Original DECT reports were classified as positive, negative, or equivocal for MSU crystals indicative of gout. Joint aspirations occurring after the DECT examinations were recorded on the basis of findings from medical record review. A single radiologist performed a post hoc retrospective blinded image review, classifying examinations as positive, negative, or equivocal. RESULTS. In 2013, 44.0% of DECT examinations were interpreted as positive, 23.0% as negative, and 33.0% as equivocal; in 2019, 37.0% were interpreted as positive, 47.0% as negative, and 16.0% as equivocal (p < .001). The frequency of joint aspiration after DECT was 14.0% in 2013 versus 2.0% in 2019 (p = .002), and that after DECT examinations with negative interpretations was 17.4% in 2013 versus 2.1% in 2019 (p = .02). In post hoc assessment by a single radiologist, the distribution of interpretations in 2013 was positive in 49.0%, negative in 22.0%, and equivocal in 29.0%, and in 2019 it was positive in 39.0%, negative in 50.0%, and equivocal in 11.0% (p < .001). CONCLUSION. When DECT examinations performed for gout in 2013 and 2019 were compared, the frequency of equivocal interpretations was significantly lower in 2019, possibly in relation to interval technologic improvements. Negative examinations were less frequently followed by joint aspirations in 2019, possibly reflecting increasing clinical acceptance of the DECT results. CLINICAL IMPACT. The findings indicate an evolving role for DECT in the evaluation of gout after an institution's routine adoption of the technology for this purpose.

Clinical evaluation of a phantom-based deep convolutional neural network for whole-body-low-dose and ultra-low-dose CT skeletal surveys.

OBJECTIVE: This study evaluated the clinical utility of a phantom-based convolutional neural network noise reduction framework for whole-body-low-dose CT skeletal surveys. MATERIALS AND METHODS: The CT exams of ten patients with multiple myeloma were retrospectively analyzed. Exams were acquired with routine whole-body-low-dose CT protocol and projection noise insertion was used to simulate 25% dose exams. Images were reconstructed with either iterative reconstruction or filtered back projection with convolutional neural network post-processing. Diagnostic quality and structure visualization were blindly rated (subjective scale ranging from 0 [poor] to 100 [excellent]) by three musculoskeletal radiologists for iterative reconstruction and convolutional neural network images at routine whole-body-low-dose and 25% dose CT. RESULTS: For the diagnostic quality rating, the convolutional neural network outscored iterative reconstruction at routine whole-body-low-dose CT (convolutional neural network: 95 ± 5, iterative reconstruction: 85 ± 8) and at the 25% dose level (convolutional neural network: 79 ± 10, iterative reconstruction: 22 ± 13). Convolutional neural network applied to 25% dose was rated inferior to iterative reconstruction applied to routine dose. Similar trends were observed in rating experiments focusing on structure visualization. CONCLUSION: Results indicate that the phantom-based convolutional neural network noise reduction framework can improve visualization of critical structures within CT skeletal surveys. At matched dose level, the convolutional neural network outscored iterative reconstruction for all conditions studied. The image quality improvement of convolutional neural network applied to 25% dose indicates a potential for dose reduction; however, the 75% dose reduction condition studied is not currently recommended for clinical implementation.

Benefits of iterative metal artifact reduction and dual-energy CT towards mitigating artifact in the setting of total shoulder prostheses.

OBJECTIVE: To determine the utility of iterative metal artifact reduction and 130 keV dual-energy virtual monoenergetic images to improve bone and soft tissue visualization in CT scans affected by metal artifacts. MATERIAL AND METHODS: Thirteen females and 6 males with a history of total shoulder prosthesis who underwent dual-energy shoulder CT were included. Four sets of images were reconstructed for each patient: (1) original polychromatic kV images reconstructed with weighted filtered back projection; (2) polychromatic kV images with iterative metal artifact reduction; (3) 130 keV dual-energy virtual monoenergetic; (4) combined iterative metal artifact reduction and 130 keV dual-energy virtual monoenergetic. Three readers blindly reviewed all image sets and graded the extent of artifact and image quality. RESULTS: Mean artifact score and median overall image quality score were better in 130 keV dual-energy virtual monoenergetic with iterative metal artifact reduction compared with those in original polychromatic kV images (3.02 vs 4.28, P < 0.001 and 3.00 vs 4.33, P < 0.001, respectively). The median difference in CT numbers between regions affected by artifacts and normal regions was lowest in 130 keV dual-energy virtual monoenergetic with iterative metal artifact reduction compared with that in original polychromatic kV images (72.28 vs 252.08, P < 0.001 for bony regions and 15.09 vs 324.38, P < 0.001 for soft tissue). CONCLUSION: In patients with metal artifacts due to shoulder replacement surgery, the use of dual-energy monoenergetic images and iterative metal artifact reduction reconstruction significantly improves both subjective and objective indicators of image quality.

Clinical evaluation of a new adaptive iterative metal artifact reduction method in whole-body low-dose CT skeletal survey examinations.

OBJECTIVE: To evaluate a new adaptive iterative metal artifact reduction algorithm (AiMAR) in whole-body low-dose CT (WBLDCT) skeletal survey examinations. METHODS: Projection data were retrospectively obtained from 25 clinical WBLDCT skeletal survey patients, each with two types of metal implants. Images were reconstructed with bone and soft tissue kernels using four settings-original and AiMAR with strengths of 2, 4, and 5. All images were anonymized and randomized for a reader study, where three musculoskeletal radiologists independently determined the overall ranking of all series based on diagnostic quality, and local scoring of metal artifact and anatomy visualization for each implant. Quantitative image noise analysis was performed in areas close to the implants. Intraclass correlation coefficients (ICC) and Krippendorff's alpha were computed for inter-rater reliability. RESULTS: AiMAR 4 was ranked the highest for 64.3% of the series across eight types of implants. For local scoring task, AiMAR 4 showed better metal artifact and anatomy visualization than the original and AiMAR 2. AiMAR 4 was comparable in anatomy visualization but inferior to AiMAR 5 in metal artifact scores. AiMAR 4 led to 56.3% noise reduction around the implant areas compared with the original images, and AiMAR 5 68.1% but also resulted in anatomy blurring in 40% of the implants. ICC and Krippendorff's alpha revealed at least substantial reliability in the local scores among the readers. CONCLUSIONS: AiMAR was evaluated in WBLDCT skeletal surveys. AiMAR 4 demonstrated the highest overall quality ranking and improved local scores with noise reduction around implant areas.

Using machine learning analyses to explore relations between eyewitness lineup looking behaviors and suspect guilt.

OBJECTIVE: We conducted 2 experiments using machine learning to better understand which lineup looking behaviors postdict suspect guilt., Hypotheses: We hypothesized that (a) lineups with guilty suspects would be subject to shorter viewing duration of all images and fewer image looks overall than lineups with innocent suspects, and (b) confidence and accuracy would be positively correlated. The question of which factors would combine to best postdict suspect guilt was exploratory. METHOD: Experiment 1 included 405 children (6-14 years; 43% female) who each made 2 eyewitness identifications after viewing 2 live targets. Experiment 2 included 342 adult participants (Mage = 21.00; females = 75%) who each made 2 identifications after viewing a video including 2 targets. Participants made identifications using an interactive touchscreen simultaneous lineup in which they were restricted to viewing one image at a time and their interaction with the lineup was recorded. RESULTS: In Experiment 1, five variables (filler look time, suspect look time, number of suspect looks, number of filler looks, and winner look time) together postdicted (with a 67% accuracy score) target presence. In Experiment 2, four variables (number of suspect looks, number of filler looks, number of loser looks, and winner looks) together postdicted (with a 73% accuracy score) target presence. CONCLUSIONS: Further exploration of witness search behaviors can provide context to identification decisions. Understanding which behaviors postdict suspect guilt may assist with interpretation of identification decisions in the same way that decision confidence is currently used. (PsycInfo Database Record (c) 2020 APA, all rights reserved).

Findings of CT-Derived Bone Strength Assessment in Inflammatory Bowel Disease Patients Undergoing CT Enterography in Clinical Practice.

BACKGROUND: Inflammatory bowel disease (IBD) patients are at risk of developing complications from metabolic bone disease, but the exact prevalence is unknown. We evaluated fracture risk in IBD patients using (1) biomechanical CT analysis (BCT) using bone strength and bone mineral density (BMD), (2) Cornerstone guidelines, and (3) other clinical features predicting fracture risk. METHODS: A retrospective review of consecutive IBD patients who underwent CT enterography (CTE) with BCT from March 2014 to March 2017 was performed. Measured outcomes were overall fracture risk classification (not increased, increased, or high) and femoral neck BMD World Health Organization classification (normal, osteopenia, or osteoporosis). RESULTS: Two hundred fifty-seven patients with IBD underwent CTE and BCT. Fracture risk was classified as not increased in 45.5% (116/255) of patients, increased in 44.7% (114/255), and high in 9.8% (25/255). Femoral neck BMD was classified as normal in 56.8% (142/250), osteopenia in 37.6% (94/250), and osteoporosis in 5.6% (14/250). In multivariate analysis, only increasing age was associated with increased fracture risk (odds ratio, 1.06; 95% confidence interval, 1.04-1.08; P < 0.001). Cornerstone guidelines were met by 35.3% (41/116), 56.1% (64/114), and 76.0% (19/25) of patients in the not increased, increased, and high-risk groups, respectively (P = 0.0001). No Cornerstone criteria were met by 40% (56/139) of patients in the increased and high-risk groups. CONCLUSIONS: Using BCT, increased or high fracture risk was detected in more than half of this cohort, the prevalence being associated with increased age. A significant proportion of patients with increased or high fracture risk did not meet Cornerstone guidelines. Therefore, IBD patients who do not meet Cornerstone guidelines may benefit from BCT screening.

Evaluation of projection- and dual-energy-based methods for metal artifact reduction in CT using a phantom study.

OBJECTIVES: Both projection and dual-energy (DE)-based methods have been used for metal artifact reduction (MAR) in CT. The two methods can also be combined. The purpose of this work was to evaluate these three MAR methods using phantom experiments for five types of metal implants. MATERIALS AND METHODS: Five phantoms representing spine, dental, hip, shoulder, and knee were constructed with metal implants. These phantoms were scanned using both single-energy (SE) and DE protocols with matched radiation output. The SE data were processed using a projection-based MAR (iMAR, Siemens) algorithm, while the DE data were processed to generate virtual monochromatic images at high keV (Mono+, Siemens). In addition, the DE images after iMAR were used to generate Mono+ images (DE iMAR Mono+). Artifacts were quantitatively evaluated using CT numbers at different regions of interest. Iodine contrast-to-noise ratio (CNR) was evaluated in the spine phantom. Three musculoskeletal radiologists and two neuro-radiologists independently ranked the artifact reduction. RESULTS: The DE Mono+ at high keV resulted in reduced artifacts but also lower iodine CNR. The iMAR method alone caused missing tissue artifacts in dental phantom. DE iMAR Mono+ caused wrong CT numbers in close proximity to the metal prostheses in knee and hip phantoms. All musculoskeletal radiologists ranked SE iMAR > DE iMAR Mono+ > DE Mono+ for knee and hip, while DE iMAR Mono+ > SE iMAR > DE Mono+ for shoulder. Both neuro-radiologists ranked DE iMAR Mono+ > DE Mono+ > SE iMAR for spine and DE Mono+ > DE iMAR Mono+ > SE iMAR for dental. CONCLUSIONS: The SE iMAR was the best choice for the hip and knee prostheses, while DE Mono+ at high keV was best for dental implants and DE iMAR Mono+ was best for spine and shoulder prostheses. Artifacts were also introduced by MAR algorithms.

Evaluation of cross-sectional and longitudinal changes in volumetric bone mineral density in postmenopausal women using single- versus dual-energy quantitative computed tomography.

Central quantitative computed tomography (QCT) is increasingly used in clinical trials and practice to assess bone mass or strength and to evaluate longitudinal changes in response to drug treatment. Current studies utilize single-energy (SE) QCT scans, which may be confounded both by the amount of bone marrow fat at baseline and changes in marrow fat over time. However, the extent to which marrow fat changes either underestimate volumetric BMD (vBMD) measurements at baseline or under-/overestimate longitudinal changes in vivo in humans remains unclear. To address this issue, 197 early postmenopausal women [median age (IQR) 56.7 (54.4-58.7) years] underwent spine and hip QCT scans at baseline and 3 years using a 128-slice dual-source dual-energy (DE) scanner. The scans were analyzed as either SE scans (100 kVp) or DE scans (100 kVp and 140 kVp), with the latter accounting for bone marrow fat. At baseline, vertebral trabecular vBMD was (median) 17.6% lower (P < 0.001) while femur neck (FN) cortical vBMD was only 3.2% lower (P < 0.001) when assessed by SE vs DE scanning. SE scanning overestimated the 3 year rate of bone loss for trabecular bone at the spine by 24.2% (P < 0.001 vs DE rates of loss) but only by 8.8% for changes in FN cortical vBMD (P < 0.001 vs DE rates of loss). The deviation between SE and DE rates of bone loss in trabecular vBMD became progressively greater as the rate of bone loss increased. These findings demonstrate that SE QCT scans underestimate trabecular vBMD and substantially overestimate rates of age-related bone loss due to ongoing conversion of red to yellow marrow. Further, the greater the rate of bone loss, the greater the overestimation of bone loss by SE scans. Although our findings are based on normal aging, recent evidence from animal studies demonstrates that the skeletal anabolic drugs teriparatide and romosozumab may markedly reduce marrow fat, perhaps accounting for the disproportionate increases in trabecular vBMD by SE QCT as compared to dual-energy X-ray absorptiometry with these agents. As such, future studies using recently available DE scanning technology that has satisfactory precision and radiation exposure are needed to evaluate changes in trabecular vBMD independent of changes in marrow fat with aging and drugs that may alter marrow fat composition.

Intramuscular fat infiltration evaluated by magnetic resonance imaging predicts the extensibility of the supraspinatus muscle.

INTRODUCTION: Rotator cuff (RC) tears result in muscle atrophy and fat infiltration within the RC muscles. An estimation of muscle quality and deformation, or extensibility, is useful in selecting the most appropriate surgical procedure. We determined if noninvasive quantitative assessment of intramuscular fat using MRI could be used to predict extensibility of the supraspinatus muscle. METHODS: Seventeen cadaveric shoulders were imaged to assess intramuscular fat infiltration. Extensibility and histological evaluations were then performed. RESULTS: Quantitative fat infiltration positively correlated with histological findings and presented a positive correlation with muscle extensibility (r = 0.69; P = 0.002). Extensibility was not significantly different between shoulders graded with a higher fat content versus those with low fat when implementing qualitative methods. DISCUSSION: A noninvasive prediction of whole-muscle extensibility may directly guide pre-operative planning to determine if the torn edge could efficiently cover the original footprint while aiding in postoperative evaluation of RC repair. Muscle Nerve 57: 129-135, 2018.

Finite element modeling of blast lung injury in sheep.

A detailed 3D finite element model (FEM) of the sheep thorax was developed to predict heterogeneous and volumetric lung injury due to blast. A shared node mesh of the sheep thorax was constructed from a computed tomography (CT) scan of a sheep cadaver, and while most material properties were taken from literature, an elastic-plastic material model was used for the ribs based on three-point bending experiments performed on sheep rib specimens. Anesthetized sheep were blasted in an enclosure, and blast overpressure data were collected using the blast test device (BTD), while surface lung injury was quantified during necropsy. Matching blasts were simulated using the sheep thorax FEM. Surface lung injury in the FEM was matched to pathology reports by setting a threshold value of the scalar output termed the strain product (maximum value of the dot product of strain and strain-rate vectors over all simulation time) in the surface elements. Volumetric lung injury was quantified by applying the threshold value to all elements in the model lungs, and a correlation was found between predicted volumetric injury and measured postblast lung weights. All predictions are made for the left and right lungs separately. This work represents a significant step toward the prediction of localized and heterogeneous blast lung injury, as well as volumetric injury, which was not recorded during field testing for sheep.

MR imaging of synovial disorders of the knee: an update.

Synovial disorders often affect the knee joint and are a common cause of morbidity. Before MR imaging, radiologists were limited in their ability to provide information about the presence or absence of synovial disease. With the advent of MR imaging, useful information can now be provided to referring clinicians, often at a time when the initiation of therapy may mitigate significantly the long-term sequelae of synovial disorders. MR imaging, owing to its superior soft-tissue contrast, is the imaging modality of choice for demonstrating and quantifying pathologic changes of the synovium. MR imaging provides invaluable information to the clinician regarding the need to either initiate or modify therapy in those patients suffering from diseases of, or affecting, the synovium.