Fraping: A computational tool for detecting slight differences in fluorescence recovery after photobleaching (FRAP) data for actin polymerization analysis

Fluorescence recovery after photobleaching (FRAP) is a laser method of light microscopy to evaluate the rapid movement of fluorescent molecules. To have a more reliable approach to analyze data from FRAP, we designed Fraping, a free access R library to data analysis obtained from FRAP. Unlike other programs, Fraping has a new form of analyzing curves of FRAP using statistical analysis based on the average curve difference. To evaluate our library, we analyzed the differences of actin polymerization in real time between dendrites and secondary neurites of cultured neuron transfected with LifeAct to track F-actin changes of neurites. We found that Fraping provided greater sensitivity than the conventional model using mobile fraction analysis. Likewise, this approach allowed us to normalize the fluorescence to the size area of interest and adjust data curves choosing the best parametric model. In addition, this library was supplemented with data simulation to have a more significant enrichment for the analysis behavior. We concluded that Fraping is a method that reduces bias when analyzing two data groups as compared with the conventional methods. This method also allows the users to choose a more suitable analysis approach according to their requirements. RESEARCH HIGHLIGHTS: Fraping is a new programming tool to analyze FRAP data to normalize fluorescence recovery curves. The conventional method uses one-point analysis, and the new one compares all the points to define the similarity of the fluorescence recovery.

Automated ASPECTS in acute ischemic stroke: comparison of the overall scores and Hounsfield unit values of two software packages and radiologists with different levels of experience

BACKGROUND

ASPECTS is a simple, rapid, and semi-quantitative method for detecting early ischemic changes (EIC). However, the agreement between software applications and neuroradiologists varies greatly.

PURPOSE

To compare ASPECTS calculated by using automated software tools to neuroradiologists evaluation in patients with acute ischemic stroke (AIS).

MATERIAL AND METHODS

Retrospectively, 61 patients with large vessel occlusion (LVO) who underwent multimodal stroke computed tomography (CT) were evaluated using two automated ASPECTS software tools (NSK and RAPID) and three neuroradiologists with different experiences (two senior neuroradiologists and one junior neuroradiologist). Four weeks later, the same three neuroradiologists re-evaluated the ASPECTS in consensus using the baseline CT and follow-up non-contrast CT (NCCT). Interclass correlation coefficients (ICCs) and Pearson correlation coefficients were applied for statistical analysis.

RESULTS

The HU value exhibited the greatest correlation in the insular lobe (r = 0.81; P < 0.001) and the lowest correlation in the internal capsule (r = 0.65; P < 0.001) between NSK and RAPID. Software analysis and human readers showed excellent agreement with the consensus reading. Compared with the consensus reading, the correlation of the two senior radiologists (ICC = 0.975 and 0.969, respectively) were higher than that of junior radiologist (ICC = 0.869), and the consistency values of the NSK and RAPID software tools after 6 h of onset to imaging (ICC = 0.894 and 0.874, respectively) were greater than those within 6 h of onset (ICC = 0.746 and 0.828, respectively).

CONCLUSION

For patients experiencing AIS due to LVO, the ASPECTS calculated with automated software agrees well with the predefined consensus score but is inferior to that of senior radiologists.

Study on Passive Heating Involving Firewalls with an Additional Sunlight Room in Rural Residential Buildings

With the growth in China’s economic GDP, energy consumption has increased year by year. The energy demand of rural residential buildings is 223 million tons of standard coal equivalent, accounting for 24% of the national energy demand. Therefore, an energy-saving design for rural residences is necessary. This research took the traditional residences in southern Shaanxi as the research object and combined the cooking methods in southern Shaanxi with solar heating, proposing a sunlight heating system with an additional firewall. The system is composed of a firewall system and a sunlight system. The combination of the two systems prolongs the heating time and makes up for the lack of intermittent heating. The firewall principle involves using the heat generated by cooking through the heat storage and heat release capacity of the wall, and using the principle of heat radiation and convection to increase the indoor temperature. Meanwhile, the principle of the additional sunlight room involves using the external facade of the building to establish an additional sunlight room, by absorbing the heat radiation of the sun and using the principle of heat transfer from the wall. The rapid loss of indoor hot air is avoided, the heating time is prolonged, and part of the heat is retained, thereby improving the heating efficiency. A model was established based on the typical residential model in southern Shaanxi, and the presence or absence of solar radiation on the wall was used as the research variable. Using ANSYS software to simulate the analysis, it is concluded that the firewall–sunlight system can extend the heating time and meet the continuous heating demand, and the heating effect is better than that of the firewall heating system alone. When the walls have solar radiation, the annual heat load reduction rate of the buildings under the new system is 20.21%. When the walls do not have solar radiation, the annual heat load reduction rate of the buildings under the new system is 8.56%.

Testing of a Program to Automatically Analyze Students' Concept Maps

Concept maps are graphical representations of how various concepts relate to one another. Assessment of concept maps developed by students in the pharmacy curriculum helps to evaluate student understanding of course material. However, providing feedback on concept maps can be time-consuming and often requires the grader to be a content expert. The purpose of this study was to develop and validate a software program to provide students with feedback on their concept map performance. Student maps for four different disease states were compared against expert concept maps. The analysis of the program compared favorably to a manual assessment of student maps for the maps' complexity and content but did not correlate for their organization. The value of using a software program to quickly and efficiently analyze concept maps is discussed.

Novel morphological multi-scale evaluation system for quality assessment of decellularized liver scaffolds

Decellularized scaffolds can serve as an excellent three-dimensional environment for cell repopulation. They maintain tissue-specific microarchitecture of extracellular matrix proteins with important spatial cues for cell adhesion, migration, growth, and differentiation. However, criteria for quality assessment of the three-dimensional structure of decellularized scaffolds are rather fragmented, usually study-specific, and mostly semi-quantitative. Thus, we aimed to develop a robust structural assessment system for decellularized porcine liver scaffolds. Five scaffolds of different quality were used to establish the new evaluation system. We combined conventional semi-quantitative scoring criteria with a quantitative scaffold evaluation based on automated image analysis. For the quantitation, we developed a specific open source software tool (ScaffAn) applying algorithms designed for texture analysis, segmentation, and skeletonization. ScaffAn calculates selected parameters characterizing structural features of porcine liver scaffolds such as the sinusoidal network. After evaluating individual scaffolds, the total scores predicted scaffold interaction with cells in terms of cell adhesion. Higher scores corresponded to higher numbers of cells attached to the scaffolds. Moreover, our analysis revealed that the conventional system could not identify fine differences between good quality scaffolds while the additional use of ScaffAn allowed discrimination. This led us to the conclusion that only using the combined score resulted in the best discrimination between different quality scaffolds. Overall, our newly defined evaluation system has the potential to select the liver scaffolds most suitable for recellularization, and can represent a step toward better success in liver tissue engineering.

Use of ICG videoangiography and FLOW 800 analysis to identify the patient-specific venous circulation and predict the effect of venous sacrifice: a retrospective study of 172 patients

OBJECTIVE The best management of veins encountered during the neurosurgical approach is still a matter of debate. Even if venous sacrifice were to lead to devastating consequences, under certain circumstances, it might prove to be desirable, enlarging the surgical field or increasing the extent of resection in tumor surgery. In this study, the authors present a large series of patients with vascular or oncological entities, in which they used indocyanine green videoangiography (ICG-VA) with FLOW 800 analysis to study the patient-specific venous flow characteristics and the management workflow in cases in which a venous sacrifice was necessary. METHODS Between May 2011 and December 2017, 1972 patients were admitted to the authors' division for tumor and/or neurovascular surgery. They retrospectively reviewed all cases in which ICG-VA and FLOW 800 were used intraoperatively with a specific target in the venous angiographic phase or for the management of venous sacrifice, and whose surgical videos and FLOW 800 analysis were available. RESULTS A total of 296 ICG-VA and FLOW 800 studies were performed intraoperatively. In all cases, the venous structures were clearly identifiable and were described according to the flow direction and speed. The authors therefore defined different patterns of presentation: arterialized veins, thrombosed veins, fast-draining veins with anterograde flow, slow-draining veins with anterograde flow, and slow-draining veins with retrograde flow. In 16 cases we also performed a temporary clipping test to predict the effect of the venous sacrifice by the identification of potential collateral circulation. CONCLUSIONS ICG-VA and FLOW 800 analysis can provide complete and real-time intraoperative information regarding patient-specific venous drainage pattern and can guide the decision-making process regarding venous sacrifice, with a possible impact on reduction of surgical complications.

Refinement of detecting atrial fibrillation in stroke patients: results from the TRACK-AF Study

BACKGROUND AND PURPOSE

Detection of occult atrial fibrillation (AF) is crucial for optimal secondary prevention in stroke patients. The AF detection rate was determined by implantable cardiac monitor (ICM) and compared to the prediction rate of the probability of incident AF by software based analysis of a continuously monitored electrocardiogram at follow-up (stroke risk analysis, SRA); an optimized AF detection algorithm is proposed by combining both tools.

METHODS

In a monocentric prospective study 105 out of 389 patients with cryptogenic stroke despite extensive diagnostic workup were investigated with two additional cardiac monitoring tools: (a) 20 months' monitoring by ICM and (b) SRA during hospitalization at the stroke unit.

RESULTS

The detection rate of occult AF was 18% by ICM (n = 19) (range 6-575 days) and 62% (n = 65) had an increased risk for AF predicted by SRA. When comparing the predictive accuracy of SRA to ICM, the sensitivity was 95%, specificity 35%, positive predictive value 27% and negative predictive value 96%. In 18 patients with AF detected by ICM, SRA also showed a medium risk for AF. Only one patient with a very low risk predicted by SRA developed AF revealed by ICM after 417 days.

CONCLUSIONS

A combination of SRA and ICM is a promising strategy to detect occult AF. SRA is reliable in predicting incident AF with a high negative predictive value. Thus, SRA may serve as a cost-effective pre-selection tool identifying patients at risk for AF who may benefit from further cardiac monitoring by ICM.

Evaluation of an Objective Striatal Analysis Program for Determining Laterality in Uptake of ¹²³I-Ioflupane SPECT Images: Comparison to Clinical Symptoms and to Visual Reads

An automated objective striatal analysis (OSA) software program was applied to dopamine transporter (123)I-ioflupane images acquired on subjects with varying severities of parkinsonism. The striatal binding ratios (SBR) of the left and right putamina (relative to the occipital lobe) were computed, and the laterality of that measure was compared with clinical symptoms and visual reads. The objective over-read of OSA was evaluated as an aid in confirming the laterality of disease onset.

METHODS

One hundred one (123)I-ioflupane scans were acquired on clinically referred subjects. SPECT images were analyzed using the OSA software, which locates the slices containing the striatal and background (occipital) structures, positions regions over the left and right caudate nuclei and putamina, and calculates the background-subtracted SBR. Seven images were uninterpretable because of patient motion or lack of visualization of the striatum. The remaining 94 scans were analyzed with OSA. Differences between left and right putaminal SBR ranged from 0% to 36.6%, with a mean of 11.4%. When the difference between the SBR of the left and right putamina was greater than 6%, the lower side was taken as the side of onset. Left-to-right differences less than 6% were considered to be nonlateralizing (symmetric). The 94 scans were reviewed independently by 3 masked expert readers. By majority consensus, abnormal findings were seen on 67 of the 94 scans, of which 46 had available clinical findings.

RESULTS

Clinically, 34 subjects presented with lateralized tremors and 12 with symmetric or no tremors. Of the 34 cases of clinically lateralized tremors, 26 (76%) were concordant with the OSA findings, 5 were disparate with OSA (15%), and in 3 the OSA results were symmetric (9%). For the same 34 patients, the visual reads were concurrent with clinical tremor findings in 24 cases (71%), 1 was disparate (3%), and 9 visual reads were symmetric (26%). Of the 9 scans deemed symmetric by readers, 4 were correctly lateralized by OSA, and of the 3 symmetric OSA results, 2 were correctly lateralized visually.

CONCLUSION

The OSA program may be a helpful aid in the interpretation of (123)I-ioflupane SPECT images for determining laterality representing the asymmetric loss of dopamine transporters in the striata. OSA offers an objective, reproducible over-read evaluation for the laterality of onset in Parkinson disease.