Dataset of cattle biometrics through muzzle images

The Cattle Biometrics Dataset is the result of a rigorous process of data collecting, encompassing a wide range of cattle photographs obtained from publicly accessible cattle markets and farms. The dataset provided contains a comprehensive collection of more than 8,000 annotated samples derived from several cow breeds. This dataset represents a valuable asset for conducting research in the field of biometric recognition. The diversity of cattle in this context includes a range of ages, genders, breeds, and environmental conditions. Every photograph is taken from different quality cameras is thoroughly annotated, with special attention given to the muzzle of the cattle, which is considered an excellent biometric characteristic. In addition to its obvious practical benefits, this dataset possesses significant potential for extensive reuse. Within the domain of computer vision, it serves as a catalyst for algorithmic advancements, whereas in the agricultural sector, it augments practises related to cattle management. Machine learning aficionados highly value the use of machine learning for the construction and experimentation of models, especially in the context of transfer learning. Interdisciplinary collaboration is actively encouraged, facilitating the advancement of knowledge at the intersections of agriculture, computer science, and data science. The Cattle Biometrics Dataset represents a valuable resource that has the potential to stimulate significant advancements in various academic disciplines, fostering ground breaking research and innovation.

Molecular tools for recording and intervention of neuronal activity

Observing the activity of neural networks is critical for the identification of learning and memory processes, as well as abnormal activities of neural circuits in disease, particularly for the purpose of tracking disease progression. Methodologies for describing the activity history of neural networks using molecular biology techniques first utilized genes expressed by active neurons, followed by the application of recently developed techniques including optogenetics and incorporation of insights garnered from other disciplines, including chemistry and physics. In this review, we will discuss ways in which molecular biological techniques used to describe the activity of neural networks have evolved along with the potential for future development.

Glass eel migration in an urbanized catchment: an integral bottleneck assessment using mark-recapture

Diadromous fish such as the European eel (Anguilla anguilla L.) are hampered by a high density of barriers in estuaries and freshwater systems. Modified and fragmented waterbodies lack tidal flows, and habitat may be less accessible and underutilized compared to free-flowing rivers and estuaries. With rising sea levels and increased occurrence of droughts, the number of barriers may further increase, implying that the need to study migration in such areas may even become more urgent worldwide. To study glass eel migration and behaviour in such highly modified water systems, a mark-recapture study was carried out in the North Sea Canal (NSC) basin, which drains into the North Sea via a large sluice complex. In total, eight uniquely tagged groups (3,797 glass eels) were released near the sluice complex, and 11 groups (2,663 glass eels) were released at inland barriers upstream over a 28 km long stretch in the NSC in spring 2018. The sluice complex attracted 10.3 million glass eel and did not block or delay their immigration. The large and diurnally intensively used coastal ship locks and allowings some saltwater intrusion, efficiently facilitated glass eel migration. Once in the NSC, water outlets from adjacent polders attracted glass eels relative proportional to the discharge of pumping stations. In the NSC, average migration speeds of 0.7 km/day (max. 1.8 km/day) were measured, and this increased with higher temperatures. Redistribution of glass eel from accumulations at inland barriers to other outlet locations was observed in both upstream and downstream directions in the NSC. Passage success and residence time ('delays' of 4.1-13.7 days) varied between the different inland barriers. Most of the glass eel, however, appears to settle in the easily accessible habitats within the brackish NSC catchment. This study combined an integral assessment of successive bottlenecks in a modified inland water system.

Sex difference in the facilitation of fear learning by prior fear conditioning

There is now ample evidence that the strength and underlying mechanisms of memory formation can be drastically altered by prior experience. However, the prior work using rodent models on this topic has used only males as subjects, and as a result, we do know whether or not the effects of prior experience on subsequent learning are similar in both sexes. As a first step towards addressing this shortcoming, rats of both sexes were given auditory fear conditioning, or fear conditioning with unsignaled shocks, followed an hour or a day later by a single pairing of light and shock. Fear memory for each experience was assessed by measuring freezing behavior to the auditory cue and fear-potentiated startle to the light. Results showed that males trained with auditory fear conditioning showed facilitated learning to the subsequent visual fear conditioning session when the two training sessions were separated by one hour or one day. Females showed evidence of facilitation in rats given auditory conditioning when they were spaced by an hour but not when they were spaced by one day. Contextual fear conditioning did not support the facilitation of subsequent learning under any conditions. These results indicate that the mechanism by which prior fear conditioning facilitates subsequent learning differs between sexes, and they set the stage for mechanistic studies to understand the neurobiological basis of this sex difference.

A NOVEL PROTOCOL FOR RAPID DEPLOYMENT OF HEART RATE DATA STORAGE TAGS IN ATLANTIC BLUEFIN TUNA THUNNUS THYNNUS REVEALS CARDIAC RESPONSES TO TEMPERATURE AND FEEDING

The Atlantic bluefin tuna (ABFT) is a highly prized species of large pelagic fish. Studies of their environmental physiology may improve understanding and management of their populations, but this is difficult for mature adults because of their large size. Biologging of heart rate holds promise in investigating physiological responses to environmental conditions in free-swimming fishes but it is very challenging to anaesthetise large ABFT for invasive surgery to place a tag in the body cavity near to the heart. We describe a novel method for rapid deployment of a commercially available heart rate tag (HR-tag) on ABFT, using an atraumatic trocar to implant it in the musculature associated with the cleithrum. We performed three sequential experiments to show that the tagging method 1) is consistently repeatable and reliable; 2) can be used successfully on commercial fishing boats and does not seem to affect fish survival, and 3) is effective for long-term deployments. In experiment 3, a tag logged heart rate over 80 days on a 60-kg ABFT held in a farm cage. The logged data showed that heart rate was sensitive to prevailing seasonal temperature and feeding events. At low temperatures, there were clear responses to feeding but these all disappeared above a threshold temperature of 25.5 °C. Overall, the results show that our method is simple, rapid and repeatable, and can be used for long term experiments to investigate physiological responses by large ABFT to environmental conditions. This article is protected by copyright. All rights reserved.

Sex difference in the facilitation of fear learning by prior fear conditioning

There is now ample evidence that the strength and underlying mechanisms of memory formation can be drastically altered by prior experience. However, the prior work using rodent models on this topic has used only males as subjects, and as a result, we do know whether or not the effects of prior experience on subsequent learning are similar in both sexes. As a first step towards addressing this shortcoming rats of both sexes were given auditory fear conditioning, or fear conditioning with unsignaled shocks, followed an hour or a day later by a single pairing of light and shock. Fear memory for each experience was assessed by measuring freezing behavior to the auditory cue and fear-potentiated startle to the light. Results showed that males trained with auditory fear conditioning showed facilitated learning to the subsequent visual fear conditioning session when the two training sessions were separated by one hour or one day. Females showed evidence of facilitation in rats given auditory conditioning when they were spaced by an hour, but not when they were spaced by one day. Contextual fear conditioning did not support the facilitation of subsequent learning under any conditions. These results indicate that the mechanism by which prior fear conditioning facilitates subsequent learning differs between sexes, and they set the stage for mechanistic studies to understand the neurobiological basis of this sex difference.

Data for non-invasive (photo) individual fish identification of multiple species

This paper describes data from five studies focused on the individual fish identification of the same species. The lateral images of five fish species are present in the dataset. The dataset's primary purpose is to provide a data to develop a non-invasive and remote method of individual fish identification using fish skin patterns, which can serve as a substitute for the common invasive fish tagging. The lateral images of the whole fish body on the homogenous background for Sumatra barb, Atlantic salmon, Sea bass, Common carp and Rainbow trout are available with automatically extracted parts of the fish with skin patterns. A different number of individuals (Sumatra barb - 43, Atlantic salmon - 330, Sea bass - 300, Common carp - 32, Rainbow trout - 1849) were photographed by the digital camera Nikon D60 under controlled conditions. The photographs of only one side of the fish with several (from 3 to 20) repetitions were taken. Common carp, Rainbow trout and Sea bass were photographed out of the water. Atlantic salmon was photographed underwater, out of the water, and the eye of the fish was photographed by the microscope camera. Sumatra barb was photographed under the water only. For all species, except Rainbow trout, the data collection was repeated after a different period (Sumatra barb - four months, Atlantic salmon - six months, Sea bass - one month, Common carp - four months) to collect the data for a study of skin patter changes (ageing). The development of the method for photo-based individual fish identification was performed on all datasets. The identification accuracy for all species for all periods was 100% using the nearest neighbour classification. Different methods for skin pattern parametrization were used. The dataset can be used to develop remote and non-invasive individual fish identification methods. The studies focused on the discrimination power of the skin pattern can benefit from it. The changes of skin patterns due to fish ageing can be explored from the dataset.

Tagging Drosophila Proteins with Genetically Encoded Fluorophores

Proteins are typically not expressed homogeneously in all cells of a complex organism. Within cells, proteins can dynamically change locations, be transported to their destinations, or be degraded upon external signals. Thus, revealing the cellular and subcellular localizations as well as the temporal dynamics of a protein provides important insights into the possible function of the studied protein. Tagging a protein of interest with a genetically encoded fluorophore enables us to follow its expression dynamics in the living organism. Here, we summarize the genetic resources available for tagged Drosophila proteins that assist in studying protein expression and dynamics. We also review the various techniques used in the past and at present to tag a protein of interest with a genetically encoded fluorophore. Comparing the pros and cons of the various techniques guides the reader to judge the suitable applications possible with these tagged proteins in Drosophila.

Seasonal Growth of the Purple Sea Urchin Heliocidaris crassispina Revealed by Sequential Fluorochrome Tagging

Many studies have applied fluorochrome tagging to examine the growth of animals with calcified skeletons, but most of them have used only a single tag to determine the annual growth rate. We used sequential fluorochrome tagging to study the seasonal growth of the purple sea urchin Heliocidaris crassispina in Hong Kong waters from February 2012 to February 2013. Sea urchins ranging from 18.9 to 42.7 mm in test diameter had a yearly growth from 0.6 to 13.0 mm. During that year, the sea urchins grew from 0.6 to 5.0 mm in test diameter during the first six months, and from 0.4 to 10.2 mm in test diameter in the second six months. The seasonal differences in growth were confirmed using the von Bertalanffy model. The growth was clear for young sea urchins, especially for individuals less than 5 years old, but was not evident for sea urchins older than 7 years. The seasonal differences in growth were probably related to the reproductive cycle and the seasonal differences in environmental conditions. Our empirical results provide the first evidence of seasonal changes in growth for H. crassispina, demonstrating the usefulness of sequential fluorochrome tagging in studying the growth of sea urchins in the field. We also identify the problem of low recovery of tagged individuals and provide recommendations to improve the tagging procedure.

Prise en charge chirurgicale du cancer épithélial de l'ovaire - première ligne et première rechute: Surgical management of epithelial ovarian cancer - first line and first relapse

Based on recently published data, these recommendations present some evolutions in the surgical management of high grade epithelial ovarian cancers. In apparently early stages (FIGO I and II), surgical staging must be undertaken to confirm the absence of both peritoneal lesions and lymph node involvement (that might change stage and management). Neoadjuvant chemotherapy is not indicated, surgical exploration should be performed upfront, by laparotomy, to reduce the risk of rupture of the primary tumor. In advanced stages, the first step is to evaluate the feasibility of primary surgery with complete tumor cytoreduction. If it appears unfeasible, 3 or 4 cycles of neoadjuvant chemotherapy are administered before interval surgey. Whether it is implemented in the primary or interval setting, surgery must be performed by experimented teams, in an approved facility, having developed a rehabilitation program. Lymph node dissection is not mandatory if no adenopathies have been identified by imaging and by peroperative palpation. At first relapse, the surgical decision must be made by a multidisciplinary team, using scores predictive of complete cytoreduction (AGO or iMODEL criteria). Similarly as in first line, the objective is to achieve resection without any residual disease. Surveillance after first-line treatment must be adapted, according to the probability of another complete cytoreduction in case of late relapse, especially in patients who benefited from primary complete surgery and maintained good performance status.

Cardiovascular magnetic resonance virtual tagging with B-spline-based free-form deformation

PURPOSE

We developed a virtual tagging technique that reconstructs tagging images using the displacement field obtained by applying B-spline free-form deformation (FFD) between diastolic images and images of other cardiac phases in cardiac cine MRI. The purpose of this study was to validate its characteristics and usefulness in phantom and patient studies.

METHODS

Digital phantoms simulating uniform and non-uniform wall motion models were created, and virtual tagging images were reconstructed with various matrix sizes and tag resolutions to evaluate the accuracy of FFD and the characteristics of the tags. In the patient study, FFD's accuracy was assessed at three levels (base, middle, and apex) in healthy patients. In patients with heart failure, virtual tagging images were compared with strain maps obtained by feature tracking and virtual tagging.

RESULTS

In the phantom study, blurring of tags was observed when tags were reconstructed with high resolution using a small matrix size. In the patient study, the accuracy of FFD was lower in the base than in the apex. Patients with heart failure had decreased distortion of the displacement field vector and virtual tags, indicating decreased local wall motion, consistent with areas of abnormalities found in strain maps.

CONCLUSION

The virtual tagging technique does not require additional imaging and can visualize regional LV motion abnormalities via deformation of the tag as well as conventional cardiovascular magnetic resonance tagging.

Multivendor comparison of global and regional 2D cardiovascular magnetic resonance feature tracking strains vs tissue tagging at 3T

BACKGROUND

Cardiovascular magnetic resonance (CMR) 2D feature tracking (FT) left ventricular (LV) myocardial strain has seen widespread use to characterize myocardial deformation. Yet, validation of CMR FT measurements remains scarce, particularly for regional strain. Therefore, we aimed to perform intervendor comparison of 3 different FT software against tagging.

METHODS

In 61 subjects (18 healthy subjects, 18 patients with chronic myocardial infarction, 15 with dilated cardiomyopathy, and 10 with LV hypertrophy due to hypertrophic cardiomyopathy or aortic stenosis) were prospectively compared global (G) and regional transmural peak-systolic Lagrangian longitudinal (LS), circumferential (CS) and radial strains (RS) by 3 FT software (cvi42, Segment, and Tomtec) among each other and with tagging at 3T. We also evaluated the ability of regional LS, CS, and RS by different FT software vs tagging to identify late gadolinium enhancement (LGE) in the 18 infarct patients.

RESULTS

GLS and GCS by all 3 software had an excellent agreement among each other (ICC = 0.94-0.98 for GLS and ICC = 0.96-0.98 for GCS respectively) and against tagging (ICC = 0.92-0.94 for GLS and ICC = 0.88-0.91 for GCS respectively), while GRS showed inconsistent agreement between vendors (ICC 0.10-0.81). For regional LS, the agreement was good (ICC = 0.68) between 2 vendors but less vs the 3rd (ICC 0.50-0.59) and moderate to poor (ICC 0.44-0.47) between all three FT software and tagging. Also, for regional CS agreement between 2 software was higher (ICC = 0.80) than against the 3rd (ICC = 0.58-0.60), and both better agreed with tagging (ICC = 0.70-0.72) than the 3rd (ICC = 0.57). Regional RS had more variation in the agreement between methods ranging from good (ICC = 0.75) to poor (ICC = 0.05). Finally, the accuracy of scar detection by regional strains differed among the 3 FT software. While the accuracy of regional LS was similar, CS by one software was less accurate (AUC 0.68) than tagging (AUC 0.80, p < 0.006) and RS less accurate (AUC 0.578) than the other two (AUC 0.76 and 0.73, p < 0.02) to discriminate segments with LGE.

CONCLUSIONS

We confirm good agreement of CMR FT and little intervendor difference for GLS and GCS evaluation, with variable agreement for GRS. For regional strain evaluation, intervendor difference was larger, especially for RS, and the diagnostic performance varied more substantially among different vendors for regional strain analysis.

Cardiac MRI Assessment of Mouse Myocardial Infarction and Regeneration

Small animal models are indispensable for cardiac regeneration research. Studies in mouse and rat models have provided important insights into the etiology and mechanisms of cardiovascular diseases and accelerated the development of therapeutic strategies. It is vitally important to be able to evaluate the therapeutic efficacy and have reliable surrogate markers for therapeutic development for cardiac regeneration research. Magnetic resonance imaging (MRI), a versatile and noninvasive imaging modality with excellent penetration depth, tissue coverage, and soft-tissue contrast, is becoming a more important tool in both clinical settings and research arenas. Cardiac MRI (CMR) is versatile, noninvasive, and capable of measuring many different aspects of cardiac functions, and, thus, is ideally suited to evaluate therapeutic efficacy for cardiac regeneration. CMR applications include assessment of cardiac anatomy, regional wall motion, myocardial perfusion, myocardial viability, cardiac function assessment, assessment of myocardial infarction, and myocardial injury. Myocardial infarction models in mice are commonly used model systems for cardiac regeneration research. In this chapter, we discuss various CMR applications to evaluate cardiac functions and inflammation after myocardial infarction.

Clinical validation of three cardiovascular magnetic resonance techniques to measure strain and torsion in patients with suspected coronary artery disease

BACKGROUND

Several cardiovascular magnetic resonance (CMR) techniques can measure myocardial strain and torsion with high accuracy. The purpose of this study was to compare displacement encoding with stimulated echoes (DENSE), tagging and feature tracking (FT) for measuring circumferential and radial myocardial strain and myocardial torsion in order to assess myocardial function and infarct scar burden both at a global and at a segmental level.

METHOD

116 patients with a high likelihood of coronary artery disease (European SCORE > 15%) underwent CMR examination including cine images, tagging, DENSE and late gadolinium enhancement (LGE) in the short axis direction. In total, 97 patients had signs of myocardial disease and 19 had no abnormalities in terms of left ventricular (LV) wall mass index, LV ejection fraction, wall motion, LGE or a history of myocardial infarction. Thirty-four patients had myocardial infarct scar with a transmural LGE extent (transmurality) that exceeded 50% of the wall thickness in at least one segment. Global circumferential strain (GCS) and global radial strain (GRS) was analyzed using FT of cine loops, deformation of tag lines or DENSE displacement.

RESULTS

DENSE and tagging both showed high sensitivity (82% and 71%) at a specificity of 80% for the detection of segments with > 50% LGE transmurality, and receiver operating characteristics (ROC) analysis showed significantly higher area under the curve-values (AUC) for DENSE (0.87) than for tagging (0.83, p < 0.001) and FT (0.66, p = 0.003). GCS correlated with global LGE when determined with DENSE (r = 0.41), tagging (r = 0.37) and FT (r = 0.15). GRS had a low but significant negative correlation with LGE; DENSE r = - 0.10, FT r = - 0.07 and tagging r = - 0.16. Torsion from DENSE and tagging had a weak correlation (- 0.20 and - 0.22 respectively) with global LGE.

CONCLUSION

Circumferential strain from DENSE detected segments with > 50% scar with a higher AUC than strain determined from tagging and FT at a segmental level. GCS and torsion computed from DENSE and tagging showed similar correlation with global scar size, while when computed from FT, the correlation was lower.

Cardiac functional magnetic resonance imaging at 7T: Image quality optimization and ultra-high field capabilities

BACKGROUND

7T cardiac magnetic resonance imaging (MRI) introduces several advantages, as well as some limitations, compared to lower-field imaging. The capabilities of ultra-high field (UHF) MRI have not been fully exploited in cardiac functional imaging.

AIM

To optimize 7T cardiac MRI functional imaging without the need for conducting B1 shimming or subject-specific tuning, which improves scan efficiency. In this study, we provide results from phantom and in vivo scans using a multi-channel transceiver modular coil.

METHODS

We investigated the effects of adding a dielectric pad at different locations next to the imaged region of interest on improving image quality in subjects with different body habitus. We also investigated the effects of adjusting the imaging flip angle in cine and tagging sequences on improving image quality, B1 field homogeneity, signal-to-noise ratio (SNR), blood-myocardium contrast-to-noise ratio (CNR), and tagging persistence throughout the cardiac cycle.

RESULTS

The results showed the capability of achieving improved image quality with high spatial resolution (0.75 mm × 0.75 mm × 2 mm), high temporal resolution (20 ms), and increased tagging persistence (for up to 1200 ms cardiac cycle duration) at 7T cardiac MRI after adjusting scan set-up and imaging parameters. Adjusting the imaging flip angle was essential for achieving optimal SNR and myocardium-to-blood CNR. Placing a dielectric pad at the anterior left position of the chest resulted in improved B1 homogeneity compared to other positions, especially in subjects with small chest size.

CONCLUSION

Improved regional and global cardiac functional imaging can be achieved at 7T MRI through simple scan set-up adjustment and imaging parameter optimization, which would allow for more streamlined and efficient UHF cardiac MRI.

Association between methylenetetrahydrofolate reductase tagging polymorphisms and susceptibility of hepatocellular carcinoma: a case-control study

Polymorphisms in one-carbon metabolism genes may influence the susceptibility to hepatocellular carcinoma (HCC). In the present study, we studied methylenetetrahydrofolate reductase (MTHFR) tagging polymorphisms in 584 HCC cases and 923 controls. Polymerase chain reaction was harnessed to detect MTHFR genotype. Overall, our results showed that genotype distribution of MTHFR rs4846048 and rs4845882 polymorphisms was not different between HCC patients and controls. MTHFR rs9651118 and rs1801133 loci were protective factors for HCC (rs9651118: CT vs. TT: adjusted odds ratio (OR) = 0.67, 95% confidence interval (CI): 0.49–0.90, P=0.008 and TC/CC vs. TT: adjusted OR = 0.70, 95% CI: 0.53–0.93, P=0.015; rs1801133: GA vs. GG: adjusted OR = 0.72, 95% CI: 0.54–0.97, P=0.031, AA/GA vs. GG: adjusted OR = 0.76, 95% CI: 0.57–0.99, P=0.045). However, MTHFR rs3753584 locus was a candidate for susceptibility to HCC (CT vs. TT: adjusted OR = 1.67, 95% CI: 1.20–2.32, P=0.003 and TC/CC vs. TT: adjusted OR = 1.59, 95% CI: 1.15–2.20, P=0.005). Results of haplotype analysis suggested that MTHFR G_rs1801133T_rs3753584G_rs4845882A_rs4846048T_rs9651118 was associated with the risk of HCC (OR = 1.55, 95% CI: 1.16–2.07, P=0.003). The power of our study also confirmed these associations (the value of power >0.80). In summary, our findings suggested that MTHFR rs3753584, rs9651118 and rs1801133 polymorphisms may affect the risk of HCC in Chinese Han population. In future, our findings should be further validated in additional case–control studies.

Visible implant elastomer (VIE) success in early larval stages of a tropical amphibian species

Animals are often difficult to distinguish at an individual level, and being able to identify individuals can be crucial in ecological or behavioral studies. In response to this challenge, biologists have developed a range of marking (tattoos, brands, toe-clips) and tagging (banding, collars, PIT, VIA, VIE) methods to identify individuals and cohorts. Animals with complex life cycles are notoriously hard to mark because of the distortion or loss of the tag across metamorphosis. In amphibians, few studies have attempted larval tagging and none have been conducted on a tropical species. Here, we present the first successful account of VIE tagging in early larval stages (Gosner stage 25) of the dyeing poison frog (Dendrobates tinctorius) coupled with a novel anesthetic (2-PHE) application for tadpoles that does not require buffering. Mean weight of individuals at time of tagging was 0.12 g, which is the smallest and developmentally youngest anuran larvae tagged to date. We report 81% tag detection over the first month of development, as well as the persistence of tags across metamorphosis in this species. Cumulative tag retention vs tag observation differed by approximately 15% across larval development demonstrating that "lost" tags can be found later in development. Tagging had no effect on tadpole growth rate or survival. Successful application of VIE tags on D. tinctorius tadpoles introduces a new method that can be applied to better understand early life development and dispersal in various tropical species.

Rotation and torsion of the left ventricle with cardiovascular magnetic resonance tagging: comparison of two analysis methods

Background

Left ventricle rotation and torsion are fundamental components of myocardial function, and several software packages have been developed for analysis of these components. The purpose of this study was to compare the suitability of two software packages with different technical principles for analysis of rotation and torsion of the left ventricle during systole.

Methods

A group of hypertrophic cardiomyopathy (HCM) patients (N = 14, age 43 ± 11 years), mutation carriers without hypertrophy (N = 10, age 34 ± 13 years), and healthy relatives (N = 12, age 43 ± 17 years) underwent a cardiovascular magnetic resonance examination, including spatial modulation of magnetization tagging sequences in basal and apical planes of the left ventricle. The tagging images were analyzed offline using a harmonic phase image analysis method with Gabor filtering and a non-rigid registration-based free-form deformation technique. Left-ventricle rotation and torsion scores were obtained from end-diastole to end-systole with both software.

Results

Analysis was successful in all cases with both software applications. End-systolic torsion values between the study groups were not statistically different with either software. End-systolic apical rotation, end-systolic basal rotation, and end-systolic torsion were consistently higher when analyzed with non-rigid registration than with harmonic phase-based analysis (p <  0.0001). End-systolic rotation and torsion values had significant correlations between the two software (p <  0.0001), most significant in the apical plane.

Conclusions

When comparing absolute values of rotation and torsion between different individuals, software-specific reference values are required. Harmonic phase flow with Gabor filtering and non-rigid registration-based methods can both be used reliably in the analysis of systolic rotation and torsion patterns of the left ventricle.

Inter-study repeatability of circumferential strain and diastolic strain rate by CMR tagging, feature tracking and tissue tracking in ST-segment elevation myocardial infarction

Strain assessment allows accurate evaluation of myocardial function and mechanics in ST-segment elevation myocardial infarction (STEMI). Strain using cardiovascular magnetic resonance (CMR) has traditionally been assessed with tagging but limitations of this technique have led to more widespread use of alternative methods, which may be more robust. We compared the inter-study repeatability of circumferential global peak-systolic strain (Ecc) and peak-early diastolic strain rate (PEDSR) derived by tagging with values obtained using novel cine-based software: Feature Tracking (FT) (TomTec, Germany) and Tissue Tracking (TT) (Circle cvi⁴², Canada) in patients following STEMI. Twenty male patients (mean age 56 ± 10 years, mean infarct size 13.7 ± 7.1% of left ventricular mass) were randomised to undergo CMR 1-5 days post-STEMI at 1.5 T or 3.0 T, repeated after ten minutes at the same field strength. Ecc and PEDSR were assessed using tagging, FT and TT. Inter-study repeatability was evaluated using Bland-Altman analyses, coefficients of variation (CoV) and intra-class correlation coefficient (ICC). Ecc (%) was significantly lower with tagging than with FT or TT at 1.5 T (- 9.5 ± 3.3 vs. - 17.5 ± 3.8 vs. -15.5 ± 5.2, respectively, p < 0.001) and 3.0 T (- 13.1 ± 1.8 vs. - 19.4 ± 2.9 vs. - 17.3 ± 2.1, respectively, p = 0.001). This was similar for PEDSR (.s^-1): 1.5 T (0.6 ± 0.2 vs. 1.5 ± 0.4 vs. 1.0 ± 0.4, for tagging, FT and TT respectively, p < 0.001) and 3.0 T (0.6 ± 0.2 vs. 1.5 ± 0.3 vs. 0.9 ± 0.3, respectively, p < 0.001). Inter-study repeatability for Ecc at 1.5 T was good for tagging and excellent for FT and TT: CoV 16.7%, 6.38%, and 8.65%, respectively. Repeatability for Ecc at 3.0 T was good for all three techniques: CoV 14.4%, 11.2%, and 13.0%, respectively. However, repeatability of PEDSR was generally lower than that for Ecc at 1.5 T (CoV 15.1%, 13.1%, and 34.0% for tagging, FT and TT, respectively) and 3.0 T (CoV 23.0%, 18.6%, and 26.2%, respectively). Following STEMI, Ecc and PEDSR are higher when measured with FT and TT than with tagging. Inter-study repeatability of Ecc is good for tagging, excellent for FT and TT at 1.5 T, and good for all three methods at 3.0 T. The repeatability of PEDSR is good to moderate at 1.5 T and moderate at 3.0 T. Cine-based methods to assess Ecc following STEMI may be preferable to tagging.

Comparison of feature tracking, fast-SENC, and myocardial tagging for global and segmental left ventricular strain

AIMS

A multitude of cardiac magnetic resonance (CMR) techniques are used for myocardial strain assessment; however, studies comparing them are limited. We sought to compare global longitudinal (GLS), circumferential (GCS), segmental longitudinal (SLS), and segmental circumferential (SCS) strain values, as well as reproducibility between CMR feature tracking (FT), tagging (TAG), and fast-strain-encoded (fast-SENC) CMR techniques.

METHODS AND RESULTS

Eighteen subjects (11 healthy volunteers and seven patients with heart failure) underwent two CMR scans (1.5T, Philips) with identical parameters. Global and segmental strain values were measured using FT (Medis), TAG (Medviso), and fast-SENC (Myocardial Solutions). Friedman's test, linear regression, Pearson's correlation coefficient, and Bland-Altman analyses were used to assess differences and correlation in measured GLS and GCS between the techniques. Two-way mixed intra-class correlation coefficient (ICC), coefficient of variance (COV), and Bland-Altman analysis were used for reproducibility assessment. All techniques correlated closely for GLS (Pearson's r: 0.86-0.92) and GCS (Pearson's r: 0.85-0.94). Intra-observer and inter-observer reproducibility was excellent in all techniques for both GLS (ICC 0.92-0.99, CoV 2.6-10.1%) and GCS (ICC 0.89-0.99, CoV 4.3-10.1%). Inter-study reproducibility was similar for all techniques for GLS (ICC 0.91-0.96, CoV 9.1-10.8%) and GCS (ICC 0.95-0.97, CoV 7.6-10.4%). Combined segmental intra-observer reproducibility was good in all techniques for SLS (ICC 0.914-0.953, CoV 12.35-24.73%) and SCS (ICC 0.885-0.978, CoV 10.76-19.66%). Combined inter-study SLS reproducibility was the worst in FT (ICC 0.329, CoV 42.99%), while fast-SENC performed the best (ICC 0.844, CoV 21.92%). TAG had the best reproducibility for combined inter-study SCS (ICC 0.902, CoV 19.08%), while FT performed the worst (ICC 0.766, CoV 32.35%). Bland-Altman analysis revealed considerable inter-technique biases for GLS (FT vs. fast-SENC 3.71%; FT vs. TAG 8.35%; and TAG vs. fast-SENC 4.54%) and GCS (FT vs. fast-SENC 2.15%; FT vs. TAG 6.92%; and TAG vs. fast-SENC 2.15%). Limits of agreement for GLS ranged from ±3.1 (TAG vs. fast-SENC) to ±4.85 (FT vs. TAG) for GLS and ±2.98 (TAG vs. fast-SENC) to ±5.85 (FT vs. TAG) for GCS.

CONCLUSIONS

We found significant differences in measured GLS and GCS between FT, TAG, and fast-SENC. Global strain reproducibility was excellent for all techniques. Acquisition-based techniques had better reproducibility than FT for segmental strain.

Myocardial tissue characterization in patients with hereditary gelsolin (AGel) amyloidosis using novel cardiovascular magnetic resonance techniques

Gelsolin (AGel) amyloidosis is a hereditary condition with common neurological effects. Myocardial involvement, especially strain, T1, or extracellular volume (ECV), in this disease has not been investigated before. Local myocardial effects and possible amyloid accumulation were the targets of interest in this study. Fifty patients with AGel amyloidosis were enrolled in the study. All patients underwent cardiovascular magnetic resonance imaging, including cine imaging, T1 mapping, tagging, and late gadolinium enhancement (LGE) imaging at 1.5 T. Results for volumetry, myocardial feature-tracking strain, rotation, torsion, native T1, ECV, and LGE were investigated. The population mean native T1 values in different segments of the left ventricle (LV) varied between 1003 and 1080 ms. Myocardial mean T1 was 1031 ± 37 ms. T1 was highest in the basal plane of the LV (1055 ± 40 ms), similarly to ECV (30.0% ± 4.4%). ECV correlated with native T1 in all LV segments (p < 0.005). Basal LGE was detected in 76% of patients, and mid-ventricular LGE in 32%. LV longitudinal strain was impaired (- 17.4% ± 2.6%), significantly decreasing apical rotation (p = 0.018) and concurrently myocardial torsion (p = 0.005). LV longitudinal strain correlated with mean T1 and ECV of different LV planes (p < 0.04; basal p < 0.01). Myocardial involvement in AGel amyloidosis is significant, but the effects are local, focusing on the basal plane of the LV.

LeishGEdit: A Method for Rapid Gene Knockout and Tagging Using CRISPR-Cas9

Postgenomic analyses of Leishmania biology benefit from rapid and precise methods for gene manipulation. Traditional methods of gene knockout or tagging by homologous recombination have limitations: they tend to be slow and require successive transfection and selection rounds to knock out multiple alleles of a gene. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems overcome these limitations. We describe here in detail a simple, rapid, and scalable method for CRISPR-Cas9-mediated gene knockout and tagging in Leishmania. This method details how to use simple PCR to generate (1) templates for single guide RNA (sgRNA) transcription in cells expressing Cas9 and T7 RNA polymerase and (2) drug-selectable editing cassettes, using a modular set of plasmids as templates. pT plasmids allow for amplification of drug resistance genes for knockouts and pPLOT plasmids provide a choice of different tags to generate N- or C-terminally tagged proteins. We describe how to use an online platform ( LeishGEdit.net ) for automated primer design and how to perform PCRs and transfections in small batches or on 96-well plates for large-scale knockout or tagging screens. This method allows generation of knockout mutants or tagged cell lines within 1 week.

2D/3D CMR tissue tracking versus CMR tagging in the assessment of spontaneous T2DM rhesus monkeys with isolated diastolic dysfunction

BACKGROUND

Spontaneous T2DM in rhesus monkeys manifests as isolated diastolic dysfunction in the early stage of diabetic cardiomyopathy, similar to humans. Myocardial deformation measurements have emerged as a superior way to measure left ventricular (LV) function in the early stage of cardiac dysfunction, making it possible to further evaluate early-stage LV dysfunction in spontaneous T2DM rhesus monkeys.

METHODS

Spontaneous T2DM rhesus monkeys with isolated diastolic dysfunction (T2DM-DD, n = 10) and corresponding nondiabetic healthy animals (ND, n = 9) were prospectively scanned for a CMR study. Circumferential and longitudinal peak systolic strain (Ecc, Ell), time to peak strain (tEcc, tEll) and peak diastolic strain rate (CSR, LSR) obtained from 2D/3D CMR-TT were compared with those obtained from CMR tagging separately. In addition, all CMR imaging protocols were performed twice in 9 ND animals to assess test-retest reproducibility.

RESULTS

Compared with the ND group, the T2DM-DD monkeys demonstrated significantly impaired LV Ecc (- 10.63 ± 3.23 vs - 14.18 ± 3.19, p < 0.05), CSR (65.50 ± 14.48 vs 65.50 ± 14.48, p < 0.01), Ell (- 9.11 ± 2.59 vs - 14.17 ± 1.68, p < 0.05), and LSR (59.43 ± 19.17 vs 108.46 ± 22.33, p < 0.01) with the tagging. Only Ecc (- 13.10 ± 2.47 vs - 19.03 ± 3.69, p < 0.01) and CSR (148.90 ± 31.27 vs 202.00 ± 51.88, p < 0.01) were significantly reduced with 2D CMR-TT, and only Ecc (- 13.77 ± 1.98 vs - 17.26 ± 3.78, p < 0.05) was significantly reduced with 3D CMR-TT. Moreover, 2D/3D CMR-TT-derived Ecc and CSR correlated with the corresponding tagging values collectively, with a statistically significant ICC value (p < 0.05). Test-retest repeatability analysis showed that most tagging-derived biomarkers had acceptable repeatability (p < 0.01). In addition, 2D CMR-TT-derived indicators were poorer than those derived from the tagging method but better than those obtained using the 3D method, with larger ICCs except for tEcc (p < 0.05).

CONCLUSIONS

LV systolic and diastolic deformations were impaired in spontaneous T2DM rhesus monkeys previously diagnosed with isolated diastolic dysfunction by echocardiography. The 2D CMR-TT-derived Ecc and CSR were effective in the evaluation of the myocardial systolic and diastolic functions of early-diabetic cardiomyopathy, with relatively higher test-retest reproducibility and acceptable correlation with the tagging method compared with the 3D CMR-TT method.

Operation and Performance of a Mass-Selective Cryogenic Linear Ion Trap

We report on the performance of a cryogenic 2D linear ion trap (cryoLIT) that is shown to be mass-selective in the temperature range of 17-295 K. As the cryoLIT is cooled, the ejection voltages during the mass instability scan decrease, which results in an effective mass shift to lower m/z relative to room temperature. This is attributed to a decrease in trap radius caused by thermal contraction. Additionally, the cryoLIT generates reproducible mass spectra from day-to-day, and is capable of performing stored waveform inverse Fourier transform (SWIFT) mass isolation of fragile N₂-tagged ions for the purpose of background-free infrared dissociation spectroscopy. Graphical Abstract ᅟ.

Facilitation of fear learning by prior and subsequent fear conditioning

Classical fear conditioning is perhaps the premier model system used to study the neurobiological basis of memory formation. Prior work has resulted in a good understanding of both the molecular mechanisms and neural circuits supporting this form of learning. However, much of what is known about these mechanisms comes from studies in which fear memory is acquired using a single, isolated training session. Given that we cannot divorce the acquisition of new information from the backdrop on which it occurs, studies are needed to determine how the acquisition of fear memory is affected by other learning events. Here, we used rats to describe the time course by which auditory fear conditioning can facilitate learning to a different fear learning event, which alone is insufficient to support long-term fear memory. First, we replicated previous findings showing that although a single trial of light and shock produces little evidence of memory, two identical trials spaced 60 min or 24 h apart support long-term memory. Next, we report that a typical auditory fear conditioning session facilitated memory formation when rats were subsequently exposed to a single trial of light and shock 60 min or 24 h, but not 4 min, later. Finally, we show that learning can be enhanced retroactively if auditory fear conditioning occurs 60 min, but not 24 h, after a single light-shock pairing. These data demonstrate that a weak fear conditioning trial can be enhanced by prior and subsequent fear conditioning depending on the timing between training events.

Regional cardiac function analysis from tagged MRI images. Comparison of techniques: Harmonic-Phase (HARP) versus Sinusoidal-Modeling (SinMod) analysis

Cardiac MRI tagging is a valuable technique for evaluating regional heart function. Currently, there are a number of different techniques for analyzing the tagged images. Specifically, k-space-based analysis techniques showed to be much faster than image-based techniques, where harmonic-phase (HARP) and sine-wave modeling (SinMod) stand as two famous techniques of the former group, which are frequently used in clinical studies. In this study, we compared HARP and SinMod and studied inter-observer variability between the two techniques for evaluating myocardial strain and apical-to-base torsion in numerical phantom, nine healthy controls, and thirty diabetic patients. Based on the ground-truth numerical phantom measurements (strain = -20% and rotation angle = -4.4°), HARP and SinMod resulted in overestimation (in absolute value terms) of strain by 1% and 5% (strain values), and of rotation angle by 0.4° and 2.0°, respectively. For the in-vivo results, global strain and torsion ranges were -10.6% to -35.3% and 1.8°/cm to 12.7°/cm in patients, and -17.8% to -32.7% and 1.8°/cm to 12.3°/cm in volunteers. On average, SinMod overestimated strain measurements by 5.7% and 5.9% (strain values) in the patients and volunteers, respectively, compared to HARP, and overestimated torsion measurements by 2.9°/cm and 2.5°/cm in the patients and volunteers, respectively, compared to HARP. Location-wise, the ranges for basal, mid-ventricular, and apical strain in patients (volunteers) were -8.4% to -31.5% (-11.6% to -33.3%), -6.3% to -37.2% (-17.8% to -33.3%), and -5.2% to -38.4% (-20.0% to -33.2%), respectively. SinMod overestimated strain in the basal, mid-ventricular, and apical slices by 4.7% (5.7%), 5.9% (5.5%), and 8.9% (6.8%), respectively, compared to HARP in the patients (volunteers). Nevertheless, there existed good correlation between the HARP and SinMod measurements. Finally, there were no significant strain or torsion measurement differences between patients and volunteers. There existed good inter-observer agreement, as all measurement differences lied within the Bland-Altman ± 2 standard-deviation (SD) difference limits. In conclusion, despite the consistency of the results by either HARP or SinMod and acceptable agreement of the generated strain and torsion patterns by both techniques, SinMod systematically overestimated the measurements compared to HARP. Under current operating conditions, the measurements from HARP and SinMod cannot be used interchangeably.

A comparison of both DENSE and feature tracking techniques with tagging for the cardiovascular magnetic resonance assessment of myocardial strain

BACKGROUND

Myocardial strain is increasingly recognized as an important assessment for myocardial function. In addition, it also improves outcome prediction. However, there is lack of standardization in strain evaluation by cardiovascular magnetic resonance (CMR). In this study we compared strain values using multiple techniques and multiple vendor products.

METHODS

Prospectively recruited patients with cardiomyopathy of diverse etiology (N = 77) and healthy controls (N = 10) underwent CMR on a 1.5 T scanner. Tagging, displacement encoding with stimulated echoes (DENSE) and balanced stead state free precession cine imaging were acquired on all subjects. A single matched mid left ventricular (LV) short axis plane was used for the comparisons of peak circumferential (Ecc) and radial strain (Err) and a 4-chamber view for longitudinal strain (Ell). Tagging images were analyzed using harmonic phase (HARP) and displacement encoding with stimulated echoes (DENSE) images using a proprietary program. Feature tracking (FT) was evaluated using 3 commercially available software from Tomtec Imaging Systems, Cardiac Image Modeller (CIM), and Circle Cardiovascular Imaging. Tagging data were used as reference. Statistic analyses were performed using paired t-test, intraclass correlation coefficient (ICC), Bland Altman limits of agreement and coefficient of variations.

RESULTS

Average LV ejection fraction was 50% (range 32 to 62%). Regional LV wall motion abnormalities were present in 48% of the analyzed planes. The average Ecc was - 13 ± 4%, - 13 ± 4%, - 16 ± 6%, - 10 ± 3% and - 14 ± 4% for tagging, DENSE, Tomtec, CIM and Circle, respectively, with the best agreement seen in DENSE and Circle with tagging. The Err was highly varied with poor agreement across the techniques, 32 ± 24%, 40 ± 28%, 47 ± 26%, 64 ± 33% and 23 ± 9% for tagging, DENSE, Tomtec, CIM and Circle, respectively. The average Ell was - 14 ± 4%, - 8 ± 3%, - 13 ± 5%, - 11 ± 3% and - 12 ± 4% for tagging, DENSE, Tomtec, CIM and Circle, respectively with the best agreement seen in Tomtec and Circle with tagging. In the intra- and inter-observer agreement analysis the reproducibility of each technique was good except for Err by HARP.

CONCLUSIONS

Small but important differences are evident in Ecc and Ell comparisons among vendors while large differences are seen in Err assessment. Our findings suggest that CMR strain values are technique and vendor dependent. Hence, it is essential to develop reference standard from each technique and analytical product for clinical use, and to sequentially compare patient data using the same software.

Behavioral and neural mechanisms by which prior experience impacts subsequent learning

Memory is often thought about in terms of its ability to recollect and store information about the past, but its function likely rests with the fact that it permits adaptation to ongoing and future experience. Thus, the brain circuitry that encodes memory must act as if stored information is likely to be modified by subsequent experience. Considerable progress has been made in identifying the behavioral and neural mechanisms supporting the acquisition and consolidation of memories, but this knowledge comes largely from studies in laboratory animals in which the training experience is presented in isolation from prior experimentally-controlled events. Given that memories are unlikely to be formed upon a clean slate, there is a clear need to understand how learning occurs upon the background of prior experience. This article reviews recent studies from an emerging body of work on metaplasticity, memory allocation, and synaptic tagging and capture, all of which demonstrate that prior experience can have a profound effect on subsequent learning. Special attention will be given to discussion of the neural mechanisms that allow past experience to affect future learning and to the time course by which past learning events can alter subsequent learning. Finally, consideration will be given to the possible significance of a non-synaptic component of the memory trace, which in some cases is likely responsible for the priming of subsequent learning and may be involved in the recovery from amnestic treatments in which the synaptic mechanisms of memory have been impaired.

Tagging fast neutrons from a 252Cf fission-fragment source

Coincidence and time-of-flight measurement techniques are employed to tag fission neutrons emitted from a ²⁵²Cf source sealed on one side with a very thin layer of Au. The source is positioned within a gaseous ⁴He scintillator detector. Together with α particles, both light and heavy fission fragments pass through the thin layer of Au and are detected. The fragments enable the corresponding fission neutrons, which are detected in a NE-213 liquid-scintillator detector, to be tagged. The resulting continuous polychromatic beam of tagged neutrons has an energy dependence that agrees qualitatively with expectations. We anticipate that this technique will provide a cost-effective means for the characterization of neutron-detector efficiency in the energy range 1-6MeV.

Cardiovascular magnetic resonance imaging to assess myocardial fibrosis in valvular heart disease

The left ventricular (LV) remodeling process associated with significant valvular heart disease (VHD) is characterized by an increase of myocardial interstitial space with deposition of collagen and loss of myofibers. These changes occur before LV systolic function deteriorates or the patient develops symptoms. Cardiovascular magnetic resonance (CMR) permits assessment of reactive fibrosis, with the use of T1 mapping techniques, and replacement fibrosis, with the use of late gadolinium contrast enhancement. In addition, functional consequences of these structural changes can be evaluated with myocardial tagging and feature tracking CMR, which assess the active deformation (strain) of the LV myocardium. Several studies have demonstrated that CMR techniques may be more sensitive than the conventional measures (LV ejection fraction or LV dimensions) to detect these structural and functional changes in patients with severe left-sided VHD and have shown that myocardial fibrosis may not be reversible after valve surgery. More important, the presence of myocardial fibrosis has been associated with lesser improvement in clinical symptoms and recovery of LV systolic function. Whether assessment of myocardial fibrosis may better select the patients with severe left-sided VHD who may benefit from surgery in terms of LV function and clinical symptoms improvement needs to be demonstrated in prospective studies. The present review article summarizes the current status of CMR techniques to assess myocardial fibrosis and appraises the current evidence on the use of these techniques for risk stratification of patients with severe aortic stenosis or regurgitation and mitral regurgitation.

Comparison of magnetic resonance feature tracking with CSPAMM HARP for the assessment of global and regional layer specific strain

PURPOSE

Layer specific strain assessment is increasingly being employed clinically. Cardiac magnetic resonance (MR) Feature Tracking (FT) is considered to be an adequate alternative for strain assessment. The aim of this study is to investigate the feasibility of FT derived layer specific strain assessment.

METHODS

CSPAMM and SSFP-Cine sequences were acquired in 38 individuals (19 patients with HFpEF, 19 controls) in identical midventricular short-axis locations. Global endocardial-, midmyocardial-, epicardial- peak systolic circumferential strain (PSCS) and regional epicardial PSCS were calculated and intra- as well inter-observer variability were assessed.

RESULTS

FT derived global epicardial and endocardial PSCS (7.9±2.3%; -19.6±4.9%) were significantly lower than tagging derived global epicardial and endocardial PSCS (-13.2±2.8%; -32.3±5.9%) (each p<0.001), while FT derived endocardial PSCS and tagging derived midmyocardial PSCS showed a strong correlation (r=0.71) and no significant differences. Global intra- and inter-observer variability of FT derived endocardial PSCS circumferential measures were acceptable (coefficient of variation 6.5% and 5.7%) while reproducibility of epicardial PSCS (coefficient of variation 16.8% and 18.1%) was poor.

CONCLUSION

The FT algorithm allows for reliable assessment of midmyocardial strain, while underestimating epicardial and endocardial strain and delivering less reproducible results than the gold standard of tagging.

Comparison of global myocardial strain assessed by cardiovascular magnetic resonance tagging and feature tracking to infarct size at predicting remodelling following STEMI

Background

To determine if global strain parameters measured by cardiovascular magnetic resonance (CMR) acutely following ST-segment Elevation Myocardial Infarction (STEMI) predict adverse left ventricular (LV) remodelling independent of infarct size (IS).

Methods

Sixty-five patients with acute STEMI (mean age 60 ± 11 years) underwent CMR at 1–3 days post-reperfusion (baseline) and at 4 months. Global peak systolic circumferential strain (GCS), measured by tagging and Feature Tracking (FT), and global peak systolic longitudinal strain (GLS), measured by FT, were calculated at baseline, along with IS. On follow up scans, volumetric analysis was performed to determine the development of adverse remodelling – a composite score based on development of either end-diastolic volume index [EDVI] ≥20% or end-systolic volume index [ESVI] ≥15% at follow-up compared to baseline.

Results

The magnitude of GCS was higher when measured using FT (−21.1 ± 6.3%) than with tagging (−12.1 ± 4.3; p < 0.001 for difference). There was good correlation of strain with baseline LVEF (r 0.64–to 0.71) and IS (ρ -0.62 to–0.72). Baseline strain parameters were unable to predict development of adverse LV remodelling. Only baseline IS predicted adverse remodelling – Odds Ratio 1.05 (95% CI 1.01–1.10, p = 0.03), area under the ROC curve 0.70 (95% CI 0.52–0.87, p = 0.04).

Conclusion

Baseline global strain by CMR does not predict the development of adverse LV remodelling following STEMI.

Removal of some common glycosylation by-products during reaction work-up

With the aim of improving the general glycosylation protocol to facilitate easy product isolation it was shown that amide by-products from glycosylation with trichloroacetimidate and N-phenyl trifluoroacetimidate donors could be removed during reaction work-up by washing with a basic aqueous solution. Excess glycosyl acceptor or lactol originating from glycosyl donor hydrolysis could equally be removed from the reaction mixture by derivatization with a basic tag and washing with an acidic solution during reaction work-up.

Residency of Reef Fish During Pile Driving Within a Shallow Pierside Environment

The potential effects of pile driving on fish populations and commercial fisheries have received significant attention given the prevalence of construction occurring in coastal habitats throughout the world. In this study, we used acoustic telemetry to assess the movement and survival of free-ranging reef fish in Port Canaveral, FL, in response to 35 days of pile driving at an existing wharf complex. The site fidelity and behavior of 15 sheepshead (Archosargus probatocephalus) and 10 gray snapper (Lutjanus griseus) were determined before, during, and after pile driving. No obvious signs of mortality or injury to tagged fish were evident from the data. There was a significant decline in the residency index for mangrove snapper at the construction wharf after pile driving compared with the baseline, although this may be influenced by natural movements of this species in the study area rather than a direct response to pile driving.

Impacts of Underwater Noise on Marine Vertebrates: Project Introduction and First Results

The project conducts application-oriented research on impacts of underwater noise on marine vertebrates in the North and Baltic Seas. In distinct subprojects, the hearing sensitivity of harbor porpoises and gray seals as well as the acoustic tolerance limit of harbor porpoises to impulsive noise from pile driving and stress reactions caused by anthropogenic noise is investigated. Animals are equipped with DTAGs capable of recording the actual surrounding noise field of free-swimming harbor porpoises and seals. Acoustic noise mapping including porpoise detectors in the Natura 2000 sites of the North and Baltic Seas will help to fully understand current noise impacts.

Global myocardial strain assessment by different imaging modalities to predict outcomes after ST-elevation myocardial infarction: A systematic review

AIM: To conduct a systematic review relating myocardial strain assessed by different imaging modalities for prognostication following ST-elevation myocardial infarction (STEMI).

METHODS: An online literature search was performed in PubMed and OVID^® electronic databases to identify any studies that assessed global myocardial strain parameters using speckle-tracking echocardiography (STE) and/or cardiac magnetic resonance imaging (CMR) techniques [either myocardial tagging or feature tracking (FT) software] in an acute STEMI cohort (days 0-14 post-event) to predict prognosis [either development of major adverse cardiac events (MACE)] or adverse left ventricular (LV) remodelling at follow-up (≥ 6 mo for MACE, ≥ 3 mo for remodelling). Search was restricted to studies within the last 20 years. All studies that matched the pre-defined search criteria were reviewed and their results interpreted. Due to considerable heterogeneity between studies, meta-analysis was not performed.

RESULTS: A total of seven studies (n = 7) were identified that matched the search criteria. All studies used STE to evaluate strain parameters - five (n = 5) assessed global longitudinal strain (GLS) (n = 5), one assessed GLS rate (GLS-R) (n = 1) and one assessed both (n = 1). Three studies showed that GLS independently predicted the development of adverse LV remodelling by multivariate analysis - odds ratio between 1.19 (CI: 1.04-1.37, P < 0.05) and 10 (CI: 6.7-14, P < 0.001) depending on the study. Four studies showed that GLS predicted the development of MACE - hazard ratio (HR) between 1.1 (CI: 1-1.1, P = 0.006) and 2.34 (1.10-4.97, P < 0.05). One paper found that GLS-R could significantly predict MACE - HR 18 (10-35, P < 0.001) - whilst another showed it did not. GLS < -10.85% had sensitivity/specificity of 89.7%/91% respectively for predicting the development of remodelling whilst GLS < -13% could predict the development of MACE with sensitivity/specificity of 100%/89% respectively. No suitable studies were identified that assessed global strain by CMR tagging or FT techniques.

CONCLUSION: GLS measured acutely post-STEMI by STE is a predictor of poor prognosis. Further research is needed to show that this is true for CMR-based techniques.

Assessment of cardiac mass from tagged magnetic resonance images

PURPOSE

Tagged and cine magnetic resonance imaging (tMRI and cMRI) techniques are used for evaluating regional and global heart function, respectively. Measuring global function parameters directly from tMRI is challenging due to the obstruction of the anatomical structure by the tagging pattern. The purpose of this study was to develop a method for processing the tMRI images to improve the myocardium-blood contrast in order to estimate global function parameters from the processed images.

MATERIALS AND METHODS

The developed method consists of two stages: (1) removing the tagging pattern based on analyzing and modeling the signal distribution in the image's k-space, and (2) enhancing the blood-myocardium contrast based on analyzing the signal intensity variability in the two tissues. The developed method is implemented on images from twelve human subjects.

RESULTS

Ventricular mass measured with the developed method showed good agreement with that measured from gold-standard cMRI images. Further, preliminary results on measuring ventricular volume using the developed method are presented.

CONCLUSION

The promising results in this study show the potential of the developed method for evaluating both regional and global heart function from a single set of tMRI images, with associated reduction in scan time and patient discomfort.

Behavioral Response of Reef Fish and Green Sea Turtles to Midfrequency Sonar

There is growing concern over the potential effects of high-intensity sonar on wild fish populations and commercial fisheries. Acoustic telemetry was employed to measure the movements of free-ranging reef fish and sea turtles in Port Canaveral, FL, in response to routine submarine sonar testing. Twenty-five sheepshead (Archosargus probatocephalus), 28 gray snapper (Lutjanus griseus), and 29 green sea turtles (Chelonia mydas) were tagged, with movements monitored for a period of up to 4 months using an array of passive acoustic receivers. Baseline residency was examined for fish and sea turtles before, during, and after the test event. No mortality of tagged fish or sea turtles was evident from the sonar test event. There was a significant increase in the daily residency index for both sheepshead and gray snapper at the testing wharf subsequent to the event. No broad-scale movement from the study site was observed during or immediately after the test.

Cine viability magnetic resonance imaging of the heart without increased scan time

Cardiac magnetic resonance imaging (MRI) provides information about myocardial morphology, function, and viability from cine, tagged, and late gadolinium enhancement (LGE) images, respectively. While the cine and tagged images are acquired in a time-resolved fashion, the LGE images are acquired at a single timeframe. The purpose of this work is to develop a method for generating cine LGE images without additional scan time. The motion field is extracted from the tagged images, and is then used to guide the deformation of the infarcted region from the acquired LGE image at the acquired timeframe to any other timeframe. Major techniques for motion estimation, including harmonic phase (HARP) and optical flow analysis, are tested in this work for motion estimation. The proposed method is tested on numerical phantom and images from four human subjects. The generated cine LGE images showed both viability and wall motion information in the same set of images without additional scan time or image misregistration problems. The band-pass optical flow analysis resulted in the most accurate motion estimation compared to other methods, especially HARP, which fails to track points at the myocardial boundary. Infarct transmurality from the generated images showed good agreement with myocardial strain, and wall thickening showed good agreement with that measured from conventional cine images. In conclusion, the developed technique allows for generating cine LGE images that enable simultaneous display of wall motion and viability information. The generated images could be useful for estimating myocardial contractility reserve and for treatment prognosis.

Proteomics equipped with multiplexing toward ultra high throughput

MS-based quantitative proteomics is a powerful technology to study virtually almost all biological and clinical samples. Although it has been known to be a high-throughput method, an MS analysis of a higher number of samples remains to be challenging practically and economically. In this issue, the use of multiplexing strategy for quantitative analysis of proteomes and phosphoproteomes has been demonstrated by Paulo et al. (Proteomics 2015, 15, 462-473) to better understand in vivo effects of two small molecule inhibitors on a mouse model. Within the short period of drug treatment, it has been found that the protein alteration is minimal in three tissues tested, whereas the phosphorylation level was widely altered.

Tackling centrosome biology through gene targeting in chicken B cells

The centrosome proteome comprises hundreds of proteins whose function at the organelle and in the cellular context is unknown. Loss-of-function studies present a powerful tool to probe the roles of these individual constituents and hence improve our insight into key questions of centrosome biology such as how centrosomes are built, how they duplicate, and which cellular processes they partake in. In cultured cells ribonucleic acid (RNA) interference remains the most widely used method to achieve protein depletion, but due to the remarkable stability of many centrosome components depletion is often incomplete. In such instances genome editing provides a viable alternative. The exceptionally high homologous recombination rate of chicken DT40 cells makes this lymphocytic cell line ideal for genetic manipulation. Here we describe methods for the design and generation of knockouts and in situ tagging of genes in these cells. Furthermore, we report an optimized technique that allows isolation of centrosomes from DT40 cells for use in in vitro functional assays and proteomic analysis. Gene editing by CRISPR-Cas9 technology is fast replacing RNA interference as a method of choice for loss-of-function studies, but the combination of the fast cell cycle, the robustness in culture and ease of gene targeting, will continue to make DT40 cells a useful model system for studies of vertebrate protein function.

Real-space imaging of macroscopic diffusion and slow flow by singlet tagging MRI

Magnetic resonance imaging can be used to study motional processes such as flow and diffusion, but the accessible timescales are limited by longitudinal relaxation. The spatially selective conversion from magnetization to long-lived singlet order in designer molecules makes it possible to tag a region of interest for an extended period of time, of the order of several minutes. Here we exploit this concept of "singlet tagging" to monitor diffusion over a macroscopic scale as well as very slow flow.

Comparison of cardiovascular magnetic resonance feature tracking and tagging for the assessment of left ventricular systolic strain in acute myocardial infarction. Eur J Radiol. 2015;84:840-848. [PMID: 25743248 DOI: 10.1016/j.ejrad.2015.02.002]

AIMS

To assess the feasibility of feature tracking (FT)-measured systolic strain post acute ST-segment elevation myocardial infarction (STEMI) and compare strain values to those obtained with tagging.

METHODS

Cardiovascular MRI at 1.5T was performed in 24 patients, 2.2 days post STEMI. Global and segmental circumferential (Ecc) and longitudinal (Ell) strain were assessed using FT and tagging, and correlated with total and segmental infarct size, area at risk and myocardial salvage.

RESULTS

All segments tracked satisfactorily with FT (p<0.001 vs. tagging). Total analysis time per patient was shorter with FT (38.2±3.8 min vs. 63.7±10.3 min, p<0.001 vs. tagging). Global Ecc and Ell were higher with FT than with tagging, apart from FT Ecc using the average of endocardial and epicardial contours (-13.45±4.1 [FT] vs. -13.85±3.9 [tagging], p=0.66). Intraobserver and interobserver agreement for global strain were excellent for FT (ICC 0.906-0.990) but interobserver agreement for tagging was lower (ICC<0.765). Interobserver and intraobserver agreement for segmental strain was good for both techniques (ICC>0.7) apart from tagging Ell, which was poor (ICC=0.15). FT-derived Ecc significantly correlated with total infarct size (r=0.44, p=0.03) and segmental infarct extent (r=0.44, p<0.01), and best distinguished transmurally infarcted segments (AUC 0.77) and infarcted from adjacent and remote segments. FT-derived Ecc correlated strongest with segmental myocardial salvage (rs=-0.406).

CONCLUSIONS

FT global Ecc and Ell measurement in acute STEMI is feasible and robust. FT-derived strain is quicker to analyse, tracks myocardium better, has better interobserver variability and correlated more strongly with infarct, area at risk (oedema), myocardial salvage and infarct transmurality.

Variation in the persistence of memory: An interplay between actin dynamics and AMPA receptors

William James noted that memories could persist from minutes to weeks. This essay attempts to explain this variation by situating the explanation in the biochemistry of dendritic spines. Two outcomes are critical to generate the synaptic basis of memory: (1) the actin cytoskeleton in the spine must be degraded to permit (2) additional AMPA receptors (GluA1s) to enter new "hot spots" in the postsynaptic density. These initial outcomes can support short-lasting memories. The threshold for these events is low but the underlying synaptic changes cannot resist the endocytic processes that remove the added AMPA receptors. For the memory to persist the degraded actin cytoskeleton must be rebuilt and the vacated "hot spots" refilled with GluA2 receptors. A primary claim is that it is the stabilization of an enlarged actin cytoskeleton that is the target outcome that consolidates the synaptic basis of memory (see Lynch et al., 2007). The stabilized actin cytoskeleton has properties that enable it to garner the synaptic proteins it needs to self sustain the potentiated state and to benefit from activation of memory modulation systems. This article is part of a Special Issue entitled Brain and Memory.

Actin dynamics and the evolution of the memory trace

The goal of this essay is to link the regulation of actin dynamics to the idea that the synaptic changes that support long-term potentiation and memory evolve in temporally overlapping stages-generation, stabilization, and consolidation. Different cellular/molecular processes operate at each stage to change the spine cytoarchitecture and, in doing so, alter its function. Calcium-dependent processes that degrade the actin cytoskeleton network promote a rapid insertion of AMPA receptors into the post synaptic density, which increases a spine's capacity to express a potentiated response to glutamate. Other post-translation events then begin to stabilize and expand the actin cytoskeleton by increasing the filament actin content of the spine and reorganizing it to be resistant to depolymerizing events. Disrupting actin polymerization during this stabilization period is a terminal event-the actin cytoskeleton shrinks and potentiated synapses de-potentiate and memories are lost. Late-arriving, new proteins may consolidate changes in the actin cytoskeleton. However, to do so requires a stabilized actin cytoskeleton. The now enlarged spine has properties that enable it to capture other newly transcribed mRNAs or their protein products and thus enable the synaptic changes that support LTP and memory to be consolidated and maintained. This article is part of a Special Issue entitled SI: Brain and Memory.

Comparison of magnetic resonance feature tracking with harmonic phase imaging analysis (CSPAMM) for assessment of global and regional diastolic function

AIMS

Complex post-processing is required for strain-derived assessment of diastolic dysfunction (DD) using CMR-tagging (TAG). Feature-tracking (FT), allows for rapid systolic strain assessment using conventional steady-state free precession (SSFP)-Cine sequences. Aim of this study was to investigate whether FT may be employed for the clinically applicable quantification of DD.

METHODS AND RESULTS

40 individuals (20 patients with DD I-III°, 20 controls) were investigated. CSPAMM and SSFP-Cine sequences were acquired in identical short-axis locations. Global and regional early diastolic strain rate (EDSR), peak diastolic strain rate (PDSR), twist, untwist and torsion were calculated from tagged and SSFP-Cine datasets. DD indices were compared, intra- as well inter-observer variability assessed.

RESULTS

for global EDSR correlated strongly (r=0.94), revealed good agreement and no significant differences between both methods. Correlation for regional EDSR was lower, results differed significantly in the anterior wall (p<0.05). Correlation for PDSR was moderate (r=0.63), results in the healthy control group differed significantly (p<0.05). FT derived rotational indices correlated poorly with TAG (twist: r=0.28; untwist: r=0.02; torsion: r=0.26), subgroup analysis revealed significant differences (p<0.05). Intra- and inter-observer variability for FT derived global EDSR and PDSR were comparable to TAG, but significantly higher for regional EDSR and rotational indices.

CONCLUSION

FT derived global EDSR allows for rapid clinical determination of diastolic dysfunction, revealing good agreement with TAG and low intra- as well as interobserver variability. However, TAG analysis not only yields higher accuracy and reproducibility of global- and regional diastolic strain, but also delivers reliable information about diastolic rotational and untwisting dynamics.

Long-lived localization in magnetic resonance imaging

The longitudinal nuclear relaxation time, T1, sets a stringent limit on the range of information that can be obtained from magnetic resonance imaging (MRI) experiments. Long-lived nuclear spin states provide a possibility to extend the timescale over which information can be encoded in magnetic resonance. We introduce a strategy to localize an ensemble of molecules for a significantly extended duration (∼30 times longer than T1 in this example), using a spatially selective conversion between magnetization and long-lived singlet order. An application to tagging and transport is proposed.

The microvascular effects of insulin resistance and diabetes on cardiac structure, function, and perfusion: a cardiovascular magnetic resonance study

Aims

Type 2 diabetes mellitus is an independent risk factor for the development of heart failure. To better understand the mechanism by which this occurs, we investigated cardiac structure, function, and perfusion in patients with and without diabetes.

Methods and results

Sixty-five patients with no stenosis >30% on invasive coronary angiography were categorized into diabetes (19) and non-diabetes (46) which was further categorized into prediabetes (30) and controls (16) according to the American Diabetes Association guidelines. Each patient underwent comprehensive cardiovascular magnetic resonance assessment. Left-ventricular (LV) mass, relative wall mass (RWM), Lagrangian circumferential strain, LV torsion, and myocardial perfusion reserve (MPR) were calculated. LV mass was higher in diabetics than non-diabetics (112.8 ± 39.7 vs. 91.5 ± 21.3 g, P = 0.01) and in diabetics than prediabetics (112.8 ± 39.7 vs. 90.3 ± 18.7 g, P = 0.02). LV torsion angle was higher in diabetics than non-diabetics (9.65 ± 1.90 vs. 8.59 ± 1.91°, P = 0.047), and MPR was lower in diabetics than non-diabetics (2.10 ± 0.76 vs. 2.84 ± 1.25 mL/g/min, P = 0.01). There was significant correlation between MPR and early diastolic strain rate (r = −0.310, P = 0.01) and LV torsion (r = −0.306, P = 0.01). In multivariable linear regression analysis, non-diabetics waist–hip ratio, but not body mass index, had a significant association with RWM (Beta = 0.34, P = 0.02).

Conclusion

Patients with diabetes have increased LV mass, LV torsion, and decreased MPR. There is a significant association between decreased MPR and increased LV torsion suggesting a possible mechanistic link between microvascular disease and cardiac dysfunction in diabetes.

Evaluation of visible implant elastomer tags in zebrafish (Danio rerio)

The use of the visible implant elastomer (VIE) tagging system in zebrafish (Danio rerio) was examined. Two tag orientations (horizontal and vertical) at the dorsal fin base were tested for tag retention, tag fragmentation and whether VIE tags affected growth and survival of juvenile zebrafish (1–4 month post hatch). Six tag locations (abdomen, anal fin base, caudal peduncle, dorsal fin base, pectoral fin base, isthmus) and 5 tag colors (yellow, red, pink, orange, blue) were evaluated for ease of VIE tag application and tag visibility in adult zebrafish. Long-term retention (1 year) and multiple tagging sites (right and left of dorsal fin and pectoral fin base) were examined in adult zebrafish. Lastly, survival of recombination activation gene 1^−/− (rag1^−/−) zebrafish was evaluated after VIE tagging.

The best tag location was the dorsal fin base, and the most visible tag color was pink. Growth rate of juvenile zebrafish was not affected by VIE tagging. Horizontal tagging is recommended in early stages of fish growth (1–2 months post hatch). VIE tags were retained for 1 year and tagging did not interfere with long-term growth and survival. There was no mortality associated with VIE tagging in rag1^−/− zebrafish.

The VIE tagging system is highly suitable for small-sized zebrafish. When familiar with the procedure, 120 adult zebrafish can be tagged in one hour. It does not increase mortality in adult zebrafish or interfere with growth in juvenile or adult zebrafish.