Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

Study on Memory Function of Stroke Patients under Exercise Relearning Based on DWI Image Analysis Based on Optimized Registration Algorithm

Objective. This paper uses an optimized registration algorithm to analyze the diffusion-weighted imaging (DWI) scan parameters of acute ischemic stroke (AIS) in the memory function of stroke patients under exercise relearning (MRP). Methods. This study used a random case-control study. 65 patients with stroke and hemiplegia were randomly divided into a control group: conventional rehabilitation intervention (32 cases), and a treatment group: MRP (33 cases). Each patient uses 4 parameters for DWI examination and obtains 4 sets of images, group 1 is the control sequence, group 2 uses parallel acquisition technology, group 3 uses parallel acquisition technology and reduces the number of excitations, group 4 uses parallel acquisition technology to reduce repetition time (TR) and echo time (TE) and enlarge the field of view, and the scan time of each group is 177, 81, 23, and 18 s in sequence. At the time of enrollment and after 12 weeks of treatment, patients in each group were evaluated with Fugl-Meyer motor function score (FMA) and modified Pap index (MBI) for hand and wrist motor function and ADL. Results. After treatment, the FMA and MBI values of the treatment group were significantly higher than those of the control group ( P < 0.05 ). Conclusion. By adopting a parallel acquisition technique and reducing the number of excitations (group 3) scanning scheme, not only the scanning time is significantly shortened, but also the image quality can meet the diagnostic requirements, which has great application value for AIS patients who need emergency treatment. MRP can obviously promote the hand and wrist motor function and daily living ability of stroke hemiplegic patients.

Multi T1-weighted contrast imaging and T1 mapping with Compressed sensing FLAWS at 3T

The Fluid And White matter Suppression (FLAWS) MRI sequence allows for the acquisition of multiple T1-weighted contrasts in a single sequence acquisition. However, its acquisition time is prohibitive for use in clinical practice when the k-space is linearly downsampled and reconstructed using the Generalized Autocalibrating Partially Parallel Acquisition (GRAPPA) technique. This study proposes a FLAWS sequence optimization tailored to allow for the acquisition of FLAWS images with a Cartesian phyllotaxis k-space undersampling and compressed sensing (CS) reconstruction at 3T. The CS FLAWS sequence parameters were determined using a method previously employed to optimize FLAWS imaging at 1.5T and 7T. In-vivo experiments show that the proposed CS FLAWS optimization allows to reduce the FLAWS sequence acquisition time from 8 mins to 6 mins without decreasing the FLAWS image quality. In addition, this study demonstrates for the first time that T1-weighted imaging with low B1 sensitivity and T1 mapping can be performed with the FLAWS sequence at 3T for both GRAPPA and CS reconstructions. The FLAWS T1 mapping was validated using in-silico, in-vitro and in-vivo experiments with comparison against the inversion recovery turbo spin echo and MP2RAGE T1 mappings. These new results suggest that the recent advances in FLAWS imaging allow to combine the MP2RAGE imaging benefits (T1-weigthed imaging with low B1 sensitivity and T1 mapping) and with the previous version of FLAWS imaging benefits (multi T1-weighted contrast imaging) in a single 6 mins sequence acquisition.

Improved Resolution and Cost Performance of Low-Cost MEMS Seismic Sensor through Parallel Acquisition

In earthquake monitoring, an important aspect of the operational effect of earthquake intensity rapid reporting and earthquake early warning networks depends on the density and performance of the deployed seismic sensors. To improve the resolution of seismic sensors as much as possible while keeping costs low, in this article the use of multiple low-cost and low-resolution digital MEMS accelerometers is proposed to increase the resolution through the correlation average method. In addition, a cost-effective MEMS seismic sensor is developed. With ARM and Linux embedded computer technology, this instrument can cyclically store the continuous collected data on a built-in large-capacity SD card for approximately 12 months. With its real-time seismic data processing algorithm, this instrument is able to automatically identify seismic events and calculate ground motion parameters. Moreover, the instrument is easy to install in a variety of ground or building conditions. The results show that the RMS noise of the instrument is reduced from 0.096 cm/s2 with a single MEMS accelerometer to 0.034 cm/s2 in a bandwidth of 0.1–20 Hz by using the correlation average method of eight low-cost MEMS accelerometers. The dynamic range reaches more than 90 dB, the amplitude–frequency response of its input and output within −3 dB is DC −80 Hz, and the linearity is better than 0.47%. In the records from our instrument, earthquakes with magnitudes between M2.2 and M5.1 and distances from the epicenter shorter than 200 km have a relatively high SNR, and are more visible than they were prior to the joint averaging.

Full Analytical Modeling Of Intrawell Chemical Tracer Concentration For Robust Production Allocation In Challenging Environments

Conventional downhole dynamic characterization is based on data from standard production logging tool (PLT) strings. Such method is not a feasible option in long horizontal drains, deep water scenarios, subsea clusters, pump-assisted wells and in presence of asphaltenes/solids deposition, mainly due to high costs and risk of tools stuck. In this respect, intrawell chemical tracers (ICT) can represent a valid and unobtrusive monitoring alternative. This paper deals with a new production allocation interpretation model of tracer concentration behavior that can overcome the limitation of standard PLT analyses in challenging environments. ICT are installed along the well completion and are characterized by a unique oil and/or water tracer signature at each selected production interval. Tracer concentration is obtained by dedicated analyses performed for each fluid sample taken at surface during transient production. Next, tracer concentration behavior over time is interpreted, for each producing interval, by means of an ad-hoc one-dimensional partial differential equation model with proper initial and boundary conditions, which describes tracer dispersion and advection profiles in such transient conditions. The full time-dependent analytical solutions are then utilized to obtain the final production allocation. The methodology has been developed and validated using data from a dozen of tracer campaigns. The approach is here presented through a selected case study, where a parallel acquisition of standard PLT and ICT data has been carried out in an offshore well. The aim was to understand if ICT could be used in substitution of the more impacting PLT for the future development wells in the field. At target, the well completion consists of a perforated production liner with tubing. The latter, which is slotted in front of the perforations, includes oil and water tracer systems. The straightforward PLT interpretation shows a clear dynamic well behavior with an oil production profile in line with the expectations from petrophysical information. Then, after a short shut-in period, the ICT-based production allocation has been performed in transient conditions with a very good match with the available outcomes from PLT: in fact, the maximum observed difference in the relative production rates is 5%. In addition, the full analytical solution of the ICT model has been fundamental to completely characterize some complex tracer concentration behaviors over time, corresponding to non-simultaneous activation of the different producing intervals. Given the consistency of the independent PLT and ICT interpretations, the monitoring campaign for the following years has been planned based on ICT only, with consequent impact on risk and cost mitigations. Although the added value of ICT is relatively well known, the successful description of the tracer signals through the full mathematical model is a novel topic and it can open the way for even more advanced applications.

Reducing SAR in 7T brain fMRI by circumventing fat suppression while removing the lipid signal through a parallel acquisition approach

Ultra-high-field functional magnetic resonance imaging (fMRI) offers a way to new insights while increasing the spatial and temporal resolution. However, a crucial concern in 7T human MRI is the increase in power deposition, supervised through the specific absorption rate (SAR). The SAR limitation can restrict the brain coverage or the minimal repetition time of fMRI experiments. In the majority of today’s studies fMRI relies on the well-known gradient-echo echo-planar imaging (GRE-EPI) sequence, which offers ultrafast acquisition. Commonly, the GRE-EPI sequence comprises two pulses: fat suppression and excitation. This work provides the means for a significant reduction in the SAR by circumventing the fat-suppression pulse. Without this fat-suppression, however, lipid signal can result in artifacts due to the chemical shift between the lipid and water signals. Our approach exploits a reconstruction similar to the simultaneous-multi-slice method to separate the lipid and water images, thus avoiding undesired lipid artifacts in brain images. The lipid-water separation is based on the known spatial shift of the lipid signal, which can be detected by the multi-channel coils sensitivity profiles. Our study shows robust human imaging, offering greater flexibility to reduce the SAR, shorten the repetition time or increase the volume coverage with substantial benefit for brain functional studies.

Reducing SAR in 7T brain fMRI by circumventing fat suppression while removing the lipid signal through a parallel acquisition approach

Ultra-high-field functional magnetic resonance imaging (fMRI) offers the way to new insights while increasing the spatial and temporal resolution. However, a crucial concern in 7T human MRI is the increase in power deposition, supervised through the specific absorption rate (SAR). The SAR limitation can restrict the brain coverage or the minimal repetition time of fMRI experiments. fMRI is based on the well-known gradient-echo echo-planar imaging (GRE-EPI) sequence, which offers ultrafast acquisition. Commonly, the GRE-EPI sequence comprises two pulses: fat suppression and excitation. This work provides the means for a significant reduction in the SAR by circumventing the fat-suppression pulse. Without this fat-suppression, however, lipid signal can result in artifacts due to the chemical shift between the lipid and water signals. Our approach exploits a reconstruction similar to the simultaneous-multi-slice (SMS) method to separate the lipid and water images, thus avoiding undesired lipid artifacts in brain images. The lipid-water separation is based on the known spatial shift of the lipid signal, which can be detected by the multi-channel coils sensitivity profiles. Our study shows robust human imaging, offering greater flexibility to reduce the SAR, shorten the repetition time or increase the volume coverage with substantial benefit for brain functional studies.