Genome sequencing of captive white tigers from Bangladesh.

OBJECTIVES: The Bengal tiger Panthera tigris tigris, is an emblematic animal for Bangladesh. Despite being the apex predator in the wild, their number is decreasing due to anthropogenic activities such as hunting, urbanization, expansion of agriculture and deforestation. By contrast, captive tigers are flourishing due to practical conservation efforts. Breeding within the small captive population can produce inbreeding depression and genetic bottlenecks, which may limit the success of conservation efforts. Despite past decades of research, a comprehensive database on genetic variation in the captive and wild Bengal tigers in Bangladesh still needs to be included. Therefore, this research aimed to investigate the White Bengal tiger genome to create a resource for future studies to understand variation underlying important functional traits. DATA DESCRIPTION: Blood samples from Chattogram Zoo were collected for three white Bengal tigers. Genomic DNA for all collected samples were extracted using a commercial DNA extraction kit. Whole genome sequencing was performed using a DNBseq platform. We generated 77 Gb of whole-genome sequencing (WGS) data for three white Bengal tigers (Average 11X coverage/sample). The data we generated will establish a paradigm for tiger research in Bangladesh by providing a genomic resource for future functional studies on the Bengal white tiger.

Feasibility Study for a Microstrip Transmission Line RF Coil Integrated with a PET Detector Module in a 7T Human MR Imaging System.

PURPOSE: The purpose of this study was to do a feasibility study on a microstrip transmission line (MS) RF coil for a positron emission tomography (PET) insert in a 7 Tesla human MRI system. The proposed MS coil integrated the RF shield of the PET detector as the ground conductor of the coil. We called the integrated module "MS PET coil." METHODS: A single-channel MS PET coil was developed with an integrated RF-shielded PET detector module. For comparison, we also studied a conventional MS coil with a single-layer ground conductor. A lutetium fine silicate (LFS) scintillation crystal block (14 × 14 × 4-layer) with a silicon photomultiplier (Hamamatsu Photonics K.K., Shizuoka, Japan) and a front-end readout circuit board were mounted inside the shield cage of the MS PET coil. The MS PET coil was studied with and without PET detectors. All three coil configurations were studied with a homogeneous phantom in a 7T MRI system (Siemens Healthineers, Erlangen, Germany). PET data measurements were conducted using a Cesium-137 radiation point source. RESULTS: The MR images were similar for the MS coil and the empty MS PET coil, as well as for the cases of MS PET coil with and without PET measurements. Compared to the empty MS PET coil (without PET detector and cable RF shield), decreases in SNR, increases in image noise and RF power, and a slight decrease in resonance frequency were seen for the case of the MS PET coil with the detector and cable shield. Differences in the PET energy histograms or in the crystal identification maps with and without MRI measurements were negligible. CONCLUSIONS: Both the MRI and PET performances of the MS PET coil showed responses that matched the MS coil responses. The performance variations of MRI data with and without PET measurement and PET data with and without MR imaging were negligible.

Study on the radiofrequency transparency of partial-ring oval-shaped prototype PET inserts in a 3 T clinical MRI system.

The purpose of this study is to evaluate the RF field responses of partial-ring RF-shielded oval-shaped positron emission tomography (PET) inserts that are used in combination with an MRI body RF coil. Partial-ring PET insert is particularly suitable for interventional investigation (e.g., trimodal PET/MRI/ultrasound imaging) and intraoperative (e.g., robotic surgery) PET/MRI studies. In this study, we used electrically floating Faraday RF shield cages to construct different partial-ring configurations of oval and cylindrical PET inserts and performed experiments on the RF field, spin echo and gradient echo images for a homogeneous phantom in a 3 T clinical MRI system. For each geometry, partial-ring configurations were studied by removing an opposing pair or a single shield cage from different positions of the PET ring. Compared to the MRI-only case, reduction in mean RF homogeneity, flip angle, and SNR for the detector opening in the first and third quadrants was approximately 13%, 15%, and 43%, respectively, whereas the values were 8%, 23%, and 48%, respectively, for the detector openings in the second and fourth quadrants. The RF field distribution also varied for different partial-ring configurations. It can be concluded that the field penetration was high for the detector openings in the first and third quadrants of both the inserts.

Application of variation theory in STEM education: A comprehensive guideline for STEM teachers.

Incorporating appropriate pedagogical strategies has been instrumental in the development of a favorable learning environment for holistic learning, particularly in Science, Technology, Engineering, and Mathematics (STEM) education. However, there is growing evidence of the need to advance the existing methods, through more robust and comprehensive fieldwork grounded in design study. It has been shown that the lack of guidance in lesson planning using variation theory is also thought to require particular attention, as the accuracy of the student learning relies significantly on the planning of the lesson. However, little research has outlined the strategy to be followed for incorporating variation theory. This article proposes a method of preparing lesson plans to systematically implement the variation theory in STEM classrooms. The method seeks to design and implement current techniques as follows:•According to variation theory, teachers must create the necessary conditions for learning for the students to recognize what they are expected to learn.•To create the necessary conditions for learning, teachers define the key aspects of the topic to be covered and use different patterns of variations in teaching those contents, such as contrast, separation, generalization, and fusion.•Finally, teachers focus on the key aspects one by one or simultaneously to grab students' attention.

MRI compatibility study of a prototype radiofrequency penetrable oval PET insert at 3 T.

PURPOSE: To perform an MRI compatibility study of an RF field-penetrable oval-shaped PET insert that implements an MRI built-in body RF coil both as a transmitter and a receiver. METHODS: Twelve electrically floating RF shielded PET detector modules were used to construct the prototype oval PET insert with a major axis of 440 mm, a minor axis of 350 mm, and an axial length of 225 mm. The electric floating of the PET detector modules was accomplished by isolating the cable shield from the detector shield using plastic tape. Studies were conducted on the transmit (B1) RF field, the image signal-to-noise ratio (SNR), and the RF pulse amplitude for a homogeneous cylindrical (diameter: 160 mm and length: 260 mm) phantom (NaCl + NiSO4 solution) in a 3 T clinical MRI system (Verio, Siemens, Erlangen, Germany). RESULTS: The B1 maps for the oval insert were similar to the MRI-only field responses. Compared to the MRI-only values, SNR reductions of 51%, 45%, and 59% were seen, respectively, for the spin echo (SE), gradient echo (GE), and echo planar (EPI) images for the case of oval PET insert. Moreover, the required RF pulse amplitudes for the SE, GE, and EPI sequences were, respectively, 1.93, 1.85, and 1.36 times larger. However, a 30% reduction in the average RF reception sensitivity was observed for the oval insert. CONCLUSIONS: The prototype floating PET insert was a safety concern for the clinical MRI system, and this compatibility study provided clearance for developing a large body size floating PET insert for the existing MRI system. Because of the RF shield of the insert, relatively large RF powers compared to the MRI-only case were required. Because of this and also due to low RF sensitivity of the body coil, the SNRs reduced largely.

Factors affecting student readiness towards OBE implementation in engineering education: Evidence from a developing country.

Engineering universities in the South Asian region have been investigating the efficacy of Outcome-Based Education (OBE) in preparing their students to meet the demands of the Fourth Industrial Revolution (4IR). Evaluating students' motivations towards OBE is crucial for its successful implementation into engineering degree programs. This research aims to explore students' readiness towards OBE implementation at one of the prominent engineering universities in Bangladesh. To achieve this aim, an instrument was developed to comprehensively measure students' readiness towards the implementation of OBE. The survey instrument with a 7-point scale, measuring six constructs of the proposed model, such as (a) Students' awareness, (b) Teachers' commitment, (c) Institutional support, (d) Perceived easiness, (e) Students' motivation, and (f) Self-efficacy, was developed and administered to a pilot sample of sixty-eight participants (N = 68) from two engineering domains: Civil and Environmental Engineering (CEE), and Computer Science and Engineering (CSE). The final data was collected from a cohort of Three Hundred and Seventy participants (N = 370), distributed across four engineering domains. A structural equation modeling (SEM) with the help of the Smart-PLS software was conducted to determine the construct validity of the measurement model and to evaluate the model fit. Results from the analysis indicate no significant positive effect of teachers' commitment (TC) on students' readiness (SR). However, the results reveal a significant positive effect of students' awareness (SA) and perceived easiness (PE) on students' readiness (SR). Results also reveal no significant moderating role of institutional support (IS) on the relation between the exogenous variables (IS, SA, PE) and the endogenous variable (SR). The research recommends Institutional Support as essential for instructors and students to implement outcome-based education (OBE) in engineering education.

Study on the radiofrequency transparency of electrically floating and ground PET inserts in a 3 T clinical MRI system.

PURPOSE: The positron emission tomography (PET) insert for a magnetic resonance imaging (MRI) system that implements the radiofrequency (RF) built-in body coil of the MRI system as a transmitter is designed to be RF-transparent, as the coil resides outside the RF-shielded PET ring. This approach reduces the design complexities (e.g., large PET ring diameter) related to implementing a transmit coil inside the PET ring. However, achieving the required field transmission into the imaging region of interest (ROI) becomes challenging because of the RF shield of the PET insert. In this study, a modularly RF-shielded PET insert is used to investigate the RF transparency considering two electrical configurations of the RF shield, namely the electrical floating and ground configurations. The purpose is to find the differences, advantages and disadvantages of these two configurations. METHODS: Eight copper-shielded PET detector modules (intermodular gap: 3 mm) were oriented cylindrically with an inner diameter of 234 mm. Each PET module included four-layer Lutetium-yttrium oxyorthosilicate scintillation crystal blocks and front-end readout electronics. RF-shielded twisted-pair cables were used to connect the front-end electronics with the power sources and PET data acquisition systems located outside the MRI room. In the ground configuration, both the detector and cable shields were connected to the RF ground of the MRI system. In the floating configuration, only the RF shields of the PET modules were isolated from the RF ground. Experiments were conducted using two cylindrical homogeneous phantoms in a 3 T clinical MRI system, in which the built-in body RF coil (a cylindrical volume coil of diameter 700 mm and length 540 mm) was implemented as a transceiver. RESULTS: For both PET configurations, the RF and MR imaging performances were lower than those for the MRI-only case, and the MRI system provided specific absorption ratio (SAR) values that were almost double. The RF homogeneity and field strength, and the signal-to-noise ratio (SNR) of the MR images were mostly higher for the floating PET configuration than they were for the ground PET configuration. However, for a shorter axial field-of-view (FOV) of 125 mm, both configurations offered almost the same performance with high RF homogeneities (e.g., 76 ± 10%). Moreover, for both PET configurations, 56 ± 6% larger RF pulse amplitudes were required for MR imaging purposes. The increased power is mostly absorbed in the conductive shields in the form of shielding RF eddy currents; as a result, the SAR values only in the phantoms were estimated to be close to the MRI-only values. CONCLUSIONS: The floating PET configuration showed higher RF transparency under all experimental setups. For a relatively short axial FOV of 125 mm, the ground configuration also performed well which indicated that an RF-penetrable PET insert with the conventional design (e.g., the ground configuration) might also become possible. However, some design modifications (e.g., a wider intermodular gap and using the RF receiver coil inside the PET insert) should improve the RF performance to the level of the MRI-only case.

Flipped classroom: How higher education institutions (HEIs) of Bangladesh could move forward during COVID-19 pandemic.

Due to COVID-19 pandemic, Bangladesh along with most of the developing countries is facing unexpected impediments towards functioning their regular activities. Most importantly, schools at all levels and Higher Educational Institutions (HEIs) have been completely shut down since March 26, 2020 that directly obliged stakeholders (Ministry of Education, institutes authorities, parents and other relevant bodies) to adopt online education. Due to having very less experience, in many cases no experience at all, of conducting teaching and learning wholly online by HEIs of Bangladesh, myriad challenges have been encountered by teachers and students. In order to find out a viable technique for dealing with these challenges, this paper addresses two research questions: What are the available open Source technologies that could be used as an alternative of paid LMS system for any developing countries during this COVID-19 pandemic? and Is exiting flipped classroom technique suitable for continuing teaching and learning during COVID-19 pandemic? In an effort to solve the above mentioned questions, a case study method was adopted. The findings of this study propose a pathway (framework) through which the HEIs of developing countries will be able to continue teaching and learning without investing money and organizing training during this COVID-19 pandemic and similar other emergency situations. This strategy provides a simple but reliable emergency means which is based on flipped classroom theory. The HEIs of Bangladesh particularly, and other developing countries generally will be benefited from this proposed framework while they do not have established means to carry their teaching and learning. This paper lastly addresses a few limitations of this framework and provides guidelines to the policymakers on how to incorporate it into the HEIs during this emergency context.

Sex-specific epidemiological and clinical characteristics of Covid-19 patients in the southeast region of Bangladesh

BackgroundCOVID-19 has become a global pandemic with a high growth rate of confirmed cases. In Bangladesh, both mortality and affected rates are increasing at an alarming rate. Therefore, more comprehensive studies of the epidemiological and clinical characteristics of COVID-19 are required to control this pandemic. PurposeThe present study aimed to compare and analyze the sex-specific epidemiological, clinical characteristics, comorbidities, and other information of confirmed COVID-19 patients from the southeast region in Bangladesh for the first time. Methods385 lab-confirmed cases were studied out of 2,471 tested samples between 5 June and 10 September 2020. RT-PCR was used for COVID-19 identification and SPSS (version 25) for statistical data analysis. ResultsWe found that male patients were roughly affected compared to females patients (male 74.30% vs. female 25.7%) with an average age of 34.86 {+/-} 15.442 years, and B (+ve) blood group has been identified as a high-risk factor for COVID-19 infection. Workplace, local market, and bank were signified as sex-specific risk zone (p < 0.001). Pre-existing medical conditions such as diabetes, hypertension, cardiovascular and respiratory diseases were identified among the patients. Less than half of the confirmed COVID-19 cases in the southeast region were asymptomatic (37.73%) and more prevalent among females than males (male vs. female: 36.84% vs. 40.51%, p = 0.001). ConclusionsThe findings may help health authorities and the government take necessary steps for identification and isolation, treatment, prevention, and control of this global pandemic.

Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning.

Genomic data analysis is a fundamental system for monitoring pathogen evolution and the outbreak of infectious diseases. Based on bioinformatics and deep learning, this study was designed to identify the genomic variability of SARS-CoV-2 worldwide and predict the impending mutation rate. Analysis of 259044 SARS-CoV-2 isolates identify 3334545 mutations (14.01 mutations per isolate), suggesting a high mutation rate. Strains from India showed the highest no. of mutations (48) followed by Scotland, USA, Netherlands, Norway, and France having up to 36 mutations. Besides the most prominently occurring mutations (D416G, F106F, P314L, and UTR:C241T), we identify L93L, A222V, A199A, V30L, and A220V mutations which are in the top 10 most frequent mutations. Multi-nucleotide mutations GGG>AAC, CC>TT, TG>CA, and AT>TA have come up in our analysis which are in the top 20 mutational cohort. Future mutation rate analysis predicts a 17%, 7%, and 3% increment of C>T, A>G, and A>T, respectively in the future. Conversely, 7%, 7%, and 6% decrement is estimated for T>C, G>A, and G>T mutations, respectively. T>G\A, C>G\A, and A>T\C are not anticipated in the future. Since SARS-CoV-2 is evolving continuously, our findings will facilitate the tracking of mutations and help to map the progression of the COVID-19 intensity worldwide.

Coping with COVID-19 Pandemic: A Population-Based Study in Bangladesh

This study aims to investigate coping strategies used by Bangladeshi citizens during the COVID-19 pandemic. DesignProspective, cross-sectional survey of adults (N=2001) living in Bangladesh. MethodsParticipants were interviewed for socio-demographic data and completed the Bengali translated Brief-COPE Inventory. Statistical data analysis was conducted using SPSS (Version 20). ResultsParticipants (N=2001), aged 18 to 86 years, were recruited from eight administrative divisions within Bangladesh (mean age 31.85{+/-}14.2 years). Male to female participant ratio was 53.4% (n=1074) to 46.6% (n=927). Higher scores were reported for approach coping styles (29.83{+/-}8.9), with lower scores reported for avoidant coping styles (20.83 {+/-} 6.05). Humor coping scores were reported at 2.68{+/-}1.3 and religion coping scores at 5.64{+/-}1.8. Both men and women showed similar coping styles. Multivariate analysis found a significant relationship between male gender and both humor and avoidant coping (p <.01). Male gender was found to be inversely related to both religion and approach coping (p <.01). Marital status and education were significantly related to all coping style domains (p<.01). Occupation was significantly related to approach coping (p <.01). Rural and urban locations differed significantly in participant coping styles (p <.01). Factor analysis revealed two cluster groups (Factor 1 and 2) comprised of unique combinations from all coping style domains. ConclusionParticipants in this study coped with the COVID-19 pandemic by utilizing a combination of coping strategies. Factor 1 revealed both avoidant and approach coping strategies and Factor 2 revealed a combination of humor and avoidant coping strategies. Overall, a higher utilization of approach coping strategies was reported, which has previously been associated with better physical and mental health outcomes. Religion was found to be a coping strategy for all participants. Future research may focus on understanding resilience in vulnerable populations, including people with disability or with migrant or refugee status in Bangladesh.

First detection of SARS-CoV-2 genetic material in the vicinity of COVID-19 isolation centre through wastewater surveillance in Bangladesh

In the course of a COVID-19 pandemic, 0.33 million people got infected in Bangladesh, we made the first and successful attempt to detect SARS-CoV-2 viruses genetic material in the vicinity wastewaters of an isolation centre i.e. Shaheed Bhulu Stadium, situated at Noakhali. The idea was to understand the genetic loading variation, both temporal and distance-wise in the nearby wastewater drains when the number of infected COVID-19 patients is not varying much. Owing to the fact that isolation center, in general, always contained a constant number of 200 COVID-19 patients, the prime objective of the study was to check if several drains carrying RNA of coronavirus are actually getting diluted or accumulated along with the sewage network. Our finding suggested that while the temporal variation of the genetic load decreased in small drains over the span of 50 days, the main sewer exhibited accumulation of SARS-CoV-2 RNA. Other interesting finding displays that probably distance of sampling location in meters is not likely to have a significant impact on gene detection concentration, although the quantity of the RNA extracted in the downstream of the drain was higher. These findings are of immense value from the perspective of wastewater surveillance of COVID-19, as they largely imply that we do not need to monitor every wastewater system, and probably major drains monitoring may illustrate the city health. Perhaps, we are reporting the accumulation of SARS-CoV-2 genetic material along the sewer network i.e. from primary to tertiary drains. The study sought further data collection in this line to simulate conditions prevailed in the most of south Asian country and to shed further light on the temporal variation and decay/accumulation processes of the genetic load of the SARS-COV-2. HIGHLIGHTSO_LIFirst detection report of SARS-CoV-2 RNA in the wastewaters of Bangladesh. C_LIO_LIWe traced the genetic load in the vicinity of the isolation center with 200 COVID-19 patients. C_LIO_LIAbout 75% of positive samples were found during the monitoring period. C_LIO_LIMain sewer and canal exhibit temporal accumulation of genetic load of SARS-CoV-2 C_LIO_LIIn general, shredding shows a variable trend during the sampling tenure. C_LI

Temporal landscape of mutation accumulation in SARS-CoV-2 genomes from Bangladesh: possible implications from the ongoing outbreak in Bangladesh

Along with intrinsic evolution, adaptation to selective pressure in new environments might have resulted in the circulatory SARS-CoV-2 strains in response to the geoenvironmental conditions of a country and the demographic profile of its population. Thus the analysis of genomic mutations of these circulatory strains may give an insight into the molecular basis of SARS-CoV-2 pathogenesis and evolution favoring the development of effective treatment and containment strategies. With this target, the current study traced the evolutionary route and mutational frequency of 198 Bangladesh originated SARS-CoV-2 genomic sequences available in the GISAID platform over a period of 13 weeks as of 14 July 2020. The analyses were performed using MEGA 7, Swiss Model Repository, Virus Pathogen Resource and Jalview visualization. Our analysis identified that majority of the circulating strains in the country belong to B and/or L type among cluster A to Z and strikingly differ from both the reference genome and the first sequenced genome from Bangladesh. Mutations in Nonspecific protein 2 (NSP2), NSP3, RNA dependent RNA polymerase (RdRp), Helicase, Spike, ORF3a, and Nucleocapsid (N) protein were common in the circulating strains with varying degrees and the most unique mutations(UM) were found in NSP3 (UM-18). But no or limited changes were observed in NSP9, NSP11, E (Envelope), NSP7a, ORF 6, and ORF 7b suggesting the possible conserved functions of those proteins in SARS-CoV-2 propagation. However, along with D614G mutation, more than 20 different mutations in the Spike protein were detected basically in the S2 domain. Besides, mutations in SR-rich region of N protein and P323L in RDRP were also present. However, the mutation accumulation showed an association with sex and age of the COVID-19 positive cases. So, identification of these mutational accumulation patterns may greatly facilitate drug/ vaccine development deciphering the age and the sex dependent differential susceptibility to COVID-19.

Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the novel coronavirus responsible for the ongoing pandemic of coronavirus disease (COVID-19). No sustainable treatment option is available so far to tackle such a public health threat. Therefore, designing a suitable vaccine to overcome this hurdle asks for immediate attention. In this study, we targeted for a design of multi-epitope based vaccine using immunoinformatics tools. We considered the structural proteins S, E and, M of SARS-CoV-2, since they facilitate the infection of the virus into host cell and using different bioinformatics tools and servers, we predicted multiple B-cell and T-cell epitopes having potential for the required vaccine design. Phylogenetic analysis provided insight on ancestral molecular changes and molecular evolutionary relationship of S, E, and M proteins. Based on the antigenicity and surface accessibility of these proteins, eight epitopes were selected by various B cell and T cell epitope prediction tools. Molecular docking was executed to interpret the binding interactions of these epitopes and three potential epitopes WTAGAAAYY, YVYSRVKNL, and GTITVEELK were selected for their noticeable higher binding affinity scores -9.1, -7.4, and -7.0 kcal/mol, respectively. Targeted epitopes had 91.09% population coverage worldwide. In summary, we identified three epitopes having the most significant properties of designing the peptide-based vaccine against SARS-CoV-2.

Microstrip Transmission Line RF Coil for a PET/MRI Insert.

PURPOSE: We proposed and developed a new microstrip transmission line radiofrequency (RF) coil for a positron emission tomography (PET) insert for MRI, which has low electrical interactions with PET shield boxes. We performed imaging experiments using a single-channel and a four-channel proposed RF coils for proof-of-concept. METHODS: A conventional microstrip coil consists of a microstrip conductor, a ground conductor, and a dielectric between the two conductors. We proposed a microstrip coil for the PET insert that replaced the conventional single-layer ground conductor with the RF shield of the PET insert. A dielectric material, which could otherwise attenuate gamma photons radiated from the PET imaging tracer, was not used. As proof-of-concept, we compared conventional and the proposed single-channel coils. To study multichannel performance, we further developed a four-channel proposed RF coil. Since the MRI system had a single-channel transmission port, an interfacing four-way RF power division circuit was designed. The coils were implemented as both RF transmitters and receivers in a cylindrical frame of diameter 150 mm. Coil bench performances were tested with a network analyzer (Rohde & Schwarz, Germany), and a homogeneous phantom study was conducted for gradient echo imaging and RF field (B1) mapping in a 3T clinical MRI system (Verio, Siemens, Erlangen, Germany). RESULTS: For all coils, the power reflection coefficient was below -30 dB, and the transmission coefficients in the four-channel configuration were near or below -20 dB. The comparative single-channel coil study showed good similarity between the conventional and proposed coils. The gradient echo image of the four-channel coil showed expected flashing image intensity near the coils and no phase distortion was visible. Transmit B1 field map resembled the image performance. CONCLUSION: The proposed PET-microstrip coil performed similarly to the conventional microstrip transmission line coil and is promising for the development of a compact coil-PET system capable of simultaneous PET/MRI analysis with an existing MRI system.

Geometry optimization of electrically floating PET inserts for improved RF penetration for a 3 T MRI system.

PURPOSE: An electrically floating radio frequency (RF) shielded PET insert with individual PET detectors shielded by separate Faraday cages enables the MRI built-in body RF coil to be used at least as an RF transmitter, in which the RF field penetrates the imaging region inside the PET ring through the narrow gaps between the shielded PET detector modules. Because the shielded PET ring blocks more than 90% of the imaging region for the transmit field from the body RF coil, it is very challenging to obtain the required RF field inside a full-ring floating PET insert. In this study, experiments were performed on the dependence of RF penetrability on different geometric aspects of the shielded PET modules and PET rings to optimize the design parameters to obtain the required RF field inside the PET ring. METHODS: We developed several prototype cylindrical full-ring PET inserts using completely enclosed empty RF shield boxes (considered as dummy PET modules). Considering the RF shield box, we conducted studies for different axial lengths (240 and 120 mm) and heights (30 and 45 mm) of the shield boxes. On the other hand, considering the PET ring geometry, we also performed studies on three different categories of PET rings: a long-ring insert (longer than the MRI phantom), a short-ring insert (shorter than the MRI phantom), and a two-ring insert that combined two short-rings. In each ring category, two different inter-shield box gaps (1 and 3 mm) were considered. In the case of the two-ring insert, three different ring-gaps (5, 10, and 20 mm) were studied. In total, 21 PET inserts were studied with an inner diameter (i.d.) of 210 mm. To study the effect of ring diameter, another long-ring insert was studied for the 270 mm i.d. Experiments were conducted for the transmit RF (B1 ) fields and signal-to-noise ratios of spin-echo and gradient-echo images using a homogeneous phantom in a 700 mm bore-diameter 3 T clinical MRI system. RF pulse amplitudes generated automatically by the MRI system were recorded for comparison. RESULTS: A PET insert with a 3 mm inter-box gap was found to perform the best, at a level which is acceptable for PET imaging. In the case of an insert of multiple short-rings instead of one long-ring insert, the 5 and 10 mm ring-gaps provided higher RF field penetration. Increasing the inter-box gap improved the RF field penetration, whereas a ring-gap that was too wide concentrated the field near the ring-gap region. Relatively reduced RF power was required for wider inter-box gap or ring-gap or larger shield box height. Moreover, the rectangular shield box outperformed the trapezoidal shield box. On the other hand, when we changed the inner or outer diameter of the PET ring by keeping the same transaxial width of the shield boxes, we did not see any noticeable variation. CONCLUSIONS: Our study results provide comprehensive guidance on the geometrical design aspects of RF-penetrable PET inserts for efficient RF penetration inside the PET ring. By choosing proper geometric design parameters, we could get the RF field that was similar to the MRI-only case.

MRI compatibility study of an integrated PET/RF-coil prototype system at 3T.

We have been working on the development of a PET insert for existing magnetic resonance imaging (MRI) systems for simultaneous PET/MR imaging, which integrates radiofrequency (RF)-shielded PET detector modules with an RF head coil. In order to avoid interferences between the PET detector circuits and the different MRI-generated electromagnetic fields, PET detector circuits were installed inside eight Cu-shielded fiber-reinforced plastic boxes, and these eight shielded PET modules were integrated in between the eight elements of a 270-mm-diameter and 280-mm-axial-length cylindrical birdcage RF coil, which was designed to be used with a 3-T clinical MRI system. The diameter of the PET scintillators with a 12-mm axial field-of-view became 255mm, which was very close to the imaging region. In this study, we have investigated the effects of this PET/RF-coil integrated system on the performance of MRI, which include the evaluation of static field (Bo) inhomogeneity, RF field (B1) distribution, local specific absorption rate (SAR) distribution, average SAR, and signal-to-noise ratio (SNR). For the central 170-mm-diameter and 80-mm-axial-length of a homogenous cylindrical phantom (with the total diameter of 200mm and axial-length of 100mm), an increase of about a maximum of 3µT in the Bo inhomogeneity was found, both in the central and 40-mm off-centered transverse planes, and a 5 percentage point increase of B1 field inhomogeneity was observed in the central transverse plane (from 84% without PET to 79% with PET), while B1 homogeneity along the coronal plane was almost unchanged (77%) following the integration of PET with the RF head coil. The average SAR and maximum local SAR were increased by 1.21 and 1.62 times, respectively. However, the SNR study for both spin-echo and gradient-echo sequences showed a reduction of about 70% and 60%, respectively, because of the shielded PET modules. The overall results prove the feasibility of this integrated PET/RF-coil system for using with the existing MRI system.

Higher sterol content regulated by CYP51 with concomitant lower phospholipid content in membranes is a common strategy for aluminium tolerance in several plant species.

Several studies have shown that differences in lipid composition and in the lipid biosynthetic pathway affect the aluminium (Al) tolerance of plants, but little is known about the molecular mechanisms underlying these differences. Phospholipids create a negative charge at the surface of the plasma membrane and enhance Al sensitivity as a result of the accumulation of positively charged Al(3+) ions. The phospholipids will be balanced by other electrically neutral lipids, such as sterols. In the present research, Al tolerance was compared among pea (Pisum sativum) genotypes. Compared with Al-tolerant genotypes, the Al-sensitive genotype accumulated more Al in the root tip, had a less intact plasma membrane, and showed a lower expression level of PsCYP51, which encodes obtusifoliol-14α-demethylase (OBT 14DM), a key sterol biosynthetic enzyme. The ratio of phospholipids to sterols was higher in the sensitive genotype than in the tolerant genotypes, suggesting that the sterol biosynthetic pathway plays an important role in Al tolerance. Consistent with this idea, a transgenic Arabidopsis thaliana line with knocked-down AtCYP51 expression showed an Al-sensitive phenotype. Uniconazole-P, an inhibitor of OBT 14DM, suppressed the Al tolerance of Al-tolerant genotypes of maize (Zea mays), sorghum (Sorghum bicolor), rice (Oryza sativa), wheat (Triticum aestivum), and triticale (×Triticosecale Wittmark cv. Currency). These results suggest that increased sterol content, regulated by CYP51, with concomitant lower phospholipid content in the root tip, results in lower negativity of the plasma membrane. This appears to be a common strategy for Al tolerance among several plant species.

Coupled circuit numerical analysis of eddy currents in an open MRI system.

We performed a new coupled circuit numerical simulation of eddy currents in an open compact magnetic resonance imaging (MRI) system. Following the coupled circuit approach, the conducting structures were divided into subdomains along the length (or width) and the thickness, and by implementing coupled circuit concepts we have simulated transient responses of eddy currents for subdomains in different locations. We implemented the Eigen matrix technique to solve the network of coupled differential equations to speed up our simulation program. On the other hand, to compute the coupling relations between the biplanar gradient coil and any other conducting structure, we implemented the solid angle form of Ampere's law. We have also calculated the solid angle for three dimensions to compute inductive couplings in any subdomain of the conducting structures. Details of the temporal and spatial distribution of the eddy currents were then implemented in the secondary magnetic field calculation by the Biot-Savart law. In a desktop computer (Programming platform: Wolfram Mathematica 8.0®, Processor: Intel(R) Core(TM)2 Duo E7500 @ 2.93GHz; OS: Windows 7 Professional; Memory (RAM): 4.00GB), it took less than 3min to simulate the entire calculation of eddy currents and fields, and approximately 6min for X-gradient coil. The results are given in the time-space domain for both the direct and the cross-terms of the eddy current magnetic fields generated by the Z-gradient coil. We have also conducted free induction decay (FID) experiments of eddy fields using a nuclear magnetic resonance (NMR) probe to verify our simulation results. The simulation results were found to be in good agreement with the experimental results. In this study we have also conducted simulations for transient and spatial responses of secondary magnetic field induced by X-gradient coil. Our approach is fast and has much less computational complexity than the conventional electromagnetic numerical simulation methods.