Investigating short-time diffusion of hyperpolarized 129 Xe in lung air spaces and tissue: A feasibility study in chronic obstructive pulmonary disease patients.

PURPOSE: To investigate the diffusion of hyperpolarized 129 Xe in air spaces at short-time scales for determination of lung surface-to-gas-volume ratio in comparison to results from chemical shift saturation recovery, CT, and established clinical measures. METHODS: A pulse sequence for measurement of time-dependent diffusion of 129 Xe in air spaces at short diffusion times was developed. Gas uptake into lung tissue was measured in the same breathhold using chemical shift saturation recovery spectroscopy in the short-time regime. The potential to obtain the surface-to-gas-volume ratio using a first-order and second-order approximation of the short-time expansion of time-dependent diffusion according to Mitra et al11 and its diagnostic relevance were tested in a study with 9 chronic obstructive pulmonary diseases patients. RESULTS: Surface-to-gas-volume ratios obtained from time-dependent diffusion were correlated with results from chemical shift saturation recovery, r = 0.840, P = .005 (first-order fits), and r = 0.923, P < .001 (second-order fits), and from CT results for second-order fits, r = 0.729, P = .026. Group means ± SD were 75.0 ± 15.5 cm-1 (first-order fits) and 122.3 ± 32.8 cm-1 (second-order fits) for time-dependent diffusion, 125.9 ± 43.3 cm-1 for chemical shift saturation recovery, and 159.5 ± 50.9 cm-1 for CT. Surface-to-gas-volume ratios from time-dependent diffusion with first-order fits correlated significantly with carbon monoxide diffusing capacity as percent of prediction, r = 0.724, P = .028. CONCLUSION: Time-dependent diffusion measurements of 129 Xe at short-time scales down to ~1 ms are feasible in chronic obstructive pulmonary patients and provide clinically relevant information on lung microstructure.

Regional investigation of lung function and microstructure parameters by localized 129 Xe chemical shift saturation recovery and dissolved-phase imaging: A reproducibility study.

PURPOSE: To evaluate the reproducibility and regional variation of parameters obtained from localized 129 Xe chemical shift saturation recovery (CSSR) MR spectroscopy in healthy volunteers and patients with chronic obstructive pulmonary disease (COPD) and to compare the results to 129 Xe dissolved-phase MR imaging. METHODS: Thirteen healthy volunteers and 10 COPD patients were scanned twice using 129 Xe dissolved-phase imaging, CSSR, and ventilation imaging sequences. A 16-channel phased-array coil in combination with the regularized spectral localization achieved by sensitivity heterogeneity (SPLASH) method was used to perform a regional analysis of CSSR data. Lung function and microstructural parameters were obtained using Patz model functions and their reproducibility was assessed. RESULTS: The Patz model alveolar wall thickness parameter shows good reproducibility on a regional basis with a median coefficient of variation of 6.5% in healthy volunteers and 12.4% in COPD patients. Significant regional differences of lung function parameters derived from localized CSSR were found in healthy volunteers and correlations with spirometric indices were found. CONCLUSION: Localized 129 Xe CSSR provides reproducible estimates of alveolar wall thickness and is able to detect regional differences of lung microstructure.

Simultaneous assessment of both lung morphometry and gas exchange function within a single breath-hold by hyperpolarized 129 Xe MRI.

During the measurement of hyperpolarized 129 Xe magnetic resonance imaging (MRI), the diffusion-weighted imaging (DWI) technique provides valuable information for the assessment of lung morphometry at the alveolar level, whereas the chemical shift saturation recovery (CSSR) technique can evaluate the gas exchange function of the lungs. To date, the two techniques have only been performed during separate breaths. However, the request for multiple breaths increases the cost and scanning time, limiting clinical application. Moreover, acquisition during separate breath-holds will increase the measurement error, because of the inconsistent physiological status of the lungs. Here, we present a new method, referred to as diffusion-weighted chemical shift saturation recovery (DWCSSR), in order to perform both DWI and CSSR within a single breath-hold. Compared with sequential single-breath schemes (namely the 'CSSR + DWI' scheme and the 'DWI + CSSR' scheme), the DWCSSR scheme is able to significantly shorten the breath-hold time, as well as to obtain high signal-to-noise ratio (SNR) signals in both DWI and CSSR data. This scheme enables comprehensive information on lung morphometry and function to be obtained within a single breath-hold. In vivo experimental results demonstrate that DWCSSR has great potential for the evaluation and diagnosis of pulmonary diseases.

Detecting pulmonary capillary blood pulsations using hyperpolarized xenon-129 chemical shift saturation recovery (CSSR) MR spectroscopy.

PURPOSE: To investigate whether chemical shift saturation recovery (CSSR) MR spectroscopy with hyperpolarized xenon-129 is sensitive to the pulsatile nature of pulmonary blood flow during the cardiac cycle. METHODS: A CSSR pulse sequence typically uses radiofrequency (RF) pulses to saturate the magnetization of xenon-129 dissolved in lung tissue followed, after a variable delay time, by an RF excitation and subsequent acquisition of a free-induction decay. Thereby it is possible to monitor the uptake of xenon-129 by lung tissue and extract physiological parameters of pulmonary gas exchange. In the current studies, the delay time was instead held at a constant value, which permitted observation of xenon-129 gas uptake as a function of breath-hold time. CSSR studies were performed in 13 subjects (10 healthy, 2 chronic obstructive pulmonary disease [COPD], 1 second-hand smoke exposure), holding their breath at total lung capacity. RESULTS: The areas of the tissue/plasma and the red-blood-cell peaks in healthy subjects varied by an average of 1.7±0.7% and 15.1±3.8%, respectively, during the cardiac cycle. In 2 subjects with COPD these peak pulsations were not detectable during at least part of the measurement period. CONCLUSION: CSSR spectroscopy is sufficiently sensitive to detect oscillations in the xenon-129 gas-uptake rate associated with the cardiac cycle.

Quantitative evaluation of radiation-induced lung injury with hyperpolarized xenon magnetic resonance.

PURPOSE: To demonstrate the feasibility of quantitative and comprehensive global evaluation of pulmonary function and microstructural changes in rats with radiation-induced lung injury (RILI) using hyperpolarized xenon MR. METHODS: Dissolved xenon spectra were dynamically acquired using a modified chemical shift saturation recovery pulse sequence in five rats with RILI (bilaterally exposed by 6-MV x-ray with a dose of 14 Gy 3 mo. prior to MR experiments) and five healthy rats. The dissolved xenon signals were quantitatively analyzed, and the pulmonary physiological parameters were extracted with the model of xenon exchange. RESULTS: The obtained pulmonary physiological parameters and the ratio of (129) Xe signal in red blood cells (RBCs) versus barrier showed a significant difference between the groups. In RILI rats versus controls, the exchange time increased from 44.5 to 112 ms, the pulmonary capillary transit time increased from 0.51 to 1.48 s, and the ratio of (129) Xe spectroscopic signal in RBCs versus barrier increased from 0.294 to 0.484. CONCLUSION: Hyperpolarized xenon MR is effective for quantitative and comprehensive global evaluation of pulmonary function and structural changes without the use of radiation. This may open the door for its use in the diagnosis of lung diseases that are related to gas exchange. Magn Reson Med 76:408-416, 2016. © 2015 Wiley Periodicals, Inc.

Assessment of lung function in asthma and COPD using hyperpolarized 129Xe chemical shift saturation recovery spectroscopy and dissolved-phase MRI.

Magnetic-resonance spectroscopy and imaging using hyperpolarized xenon-129 show great potential for evaluation of the most important function of the human lung -- gas exchange. In particular, chemical shift saturation recovery (CSSR) xenon-129 spectroscopy provides important physiological information for the lung as a whole by characterizing the dynamic process of gas exchange, while dissolved-phase (DP) xenon-129 imaging captures the time-averaged regional distribution of gas uptake by lung tissue and blood. Herein, we present recent advances in assessing lung function using CSSR spectroscopy and DP imaging in a total of 45 subjects (23 healthy, 13 chronic obstructive pulmonary disease (COPD) and 9 asthma). From CSSR acquisitions, the COPD subjects showed red blood cell to tissue-plasma (RBC-to-TP) ratios below the average for the healthy subjects (p < 0.001), but significantly higher septal wall thicknesses as compared with the healthy subjects (p < 0.005); the RBC-to-TP ratios for the asthmatic subjects fell outside two standard deviations (either higher or lower) from the mean of the healthy subjects, although there was no statistically significant difference for the average ratio of the study group as a whole. Similarly, from the 3D DP imaging acquisitions, we found that all the ratios (TP to gas phase (GP), RBC to GP, RBC to TP) measured in the COPD subjects were lower than those from the healthy subjects (p < 0.05 for all ratios), while these ratios in the asthmatic subjects differed considerably between subjects. Despite having been performed at different lung inflation levels, the RBC-to-TP ratios measured by CSSR and 3D DP imaging were fairly consistent with each other, with a mean difference of 0.037 (ratios from 3D DP imaging larger). In ten subjects the RBC-to-GP ratios obtained from the 3D DP imaging acquisitions were also highly correlated with their diffusing capacity of the lung for carbon monoxide per unit alveolar volume ratios measured by pulmonary function testing (R = 0.91).

Design and performances improvement of an UWB antenna with DGS structure using a grey wolf optimization algorithm.

In this article, we propose the design of a rectangular-shaped patch antenna suitable for ultra-wideband (UWB) applications and short and long-range Millimeter-Wave Communications. We begin with the design of a high-gain UWB rectangular patch antenna featuring a partial ground plane and operating within the 3.1-10.6 GHz bandwidth. Complementary Split Ring Resonators (CSRRs) are integrated on both sides of the structure to meet desired specifications. The resulting UWB antenna boasts an extended frequency bandwidth, covering 2.38-22.5 GHz (twice that of the original antenna), with a peak gain of 6.5 dBi and an 88% radiation efficiency. The grey wolf optimization technique (GWO) determines optimal structural dimensions. Validation of the antenna's performance is demonstrated through the strong agreement between measurement and simulation.

The role of the transcriptional repressor CssR in Corynebacterium glutamicum in response to phenolic compounds.

The cssR gene (ncgl1578) of Corynebacterium glutamicum encodes a repressor of the TetR (tetracycline regulator) family. Its role in the stress response to antibiotics/heavy metals has been investigated, but how CssR functions in response to phenolic compounds in C. glutamicum has been rarely studied. In this study, we applied transcriptomic analysis, ß-galactosidase analysis, qRT-PCR, and EMSAs to analyze the target genes and functions of CssR in response to phenolic compounds. Consistent with the upregulation of genes involved in the degradation of phenolic compounds, the ΔcssR mutant was more resistant to various phenolic compounds than was the wild-type strain. Furthermore, the addition of phenolic compounds induced the expression of corresponding genes (ncgl0283, ncgl1032, ncgl1111, ncgl2920, ncgl2923, and ncgl2952) in vivo. However, the DNA binding activity of CssR to the promoter of phenolic compound-degrading genes was undetected in vitro. Additionally, we also found that CssR indirectly negatively regulates the expression of cell wall/membrane/envelope biogenesis-related genes, which may enhance resistance to stress caused by phenolic compounds. Together, our findings demonstrate that CssR is a key regulator that copes with stress conditions induced by phenolic compounds, thus greatly expanding our understanding of the functions of TetR family transcription factors.

Genome-wide identification and characterization of microsatellite markers within the Avipoxviruses.

Microsatellite markers or Simple Sequence Repeats (SSRs) are gaining importance for molecular characterization of the virus as well as estimation of evolution patterns due to its high-polymorphic nature. The Avipoxvirus is the causative agent of pox-like lesions in more than 300 birds and one of the major diseases for the extinction of endangered avian species. Therefore, we conducted a genome-wide analysis to decipher the type, distribution pattern of 14 complete genomes derived from the Avipoxvirus genus. The in-silico screening deciphered the existence of 917-2632 SSRs per strain. In the case of compound SSRs (cSSRs), the value was obtained 44-255 per genome. Our analysis indicates that the di-nucleotide repeats (52.74%) are the most abundant, followed by the mononucleotides (34.79), trinucleotides (11.57%), tetranucleotides (0.64%), pentanucleotides (0.12%) and hexanucleotides (0.15%) repeats. The specific parameters like Relative Abundance (RA) and Relative Density (RD) of microsatellites ranged within 5.5-8.12 and 33.08-53.58 bp/kb. The analysis of RA and RD value of compound microsatellites resulted between 0.25-0.82 and 4.64-15.12 bp/kb. The analysis of motif composition of cSSR revealed that most of the compound microsatellites were made up of two microsatellites, with some unique duplicated pattern of the motif like, (TA)-x-(TA), (TCA)-x-(TCA), etc. and self-complementary motifs, such as (TA)-x-(AT). Finally, we validated forty sets of compound microsatellite markers through an in-vitro approach utilizing clinical specimens and mapping the sequencing products with the database through comparative genomics approaches. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03169-4.

CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures.

RNA secondary-structure (rSS) assignment is one of the most routine forms of analysis of RNA 3D structures. However, traditional rSS assignment programs require full-atomic structures of the individual RNA nucleotides. This prevents their application to the modeling of RNA structures in which base atoms are missing. To address this issue, Coarse-grained Secondary Structure of RNA (CSSR), an algorithm for the assignment of rSS for structures in which nucleobase atomic positions are incomplete, has been developed. Using CSSR, an rSS assignment accuracy of ∼90% is achieved even for RNA structures in which only one backbone atom per nucleotide is known. Thus, CSSR will be useful for the analysis of experimentally determined and computationally predicted RNA 3D structures alike. The source code of CSSR is available at https://github.com/pylelab/CSSR.

Machine-Learning-Guided Identification of Coordination Polymer Ligands for Crystallizing Separation of Cs/Sr.

Separation of Cs/Sr is one of many coordination-chemistry-centered processes in the grand scheme of spent nuclear fuel reprocessing, a critical link for a sustainable nuclear energy industry. To deploy a crystallizing Cs/Sr separation technology, we planned to systematically screen and identify candidate ligands that can efficiently and selectively bind to Sr2+ and form coordination polymers. Therefore, we mined the Cambridge Structural Database for characteristic structural information and developed a machine-learning-guided methodology for ligand evaluation. The optimized machine-learning model, correlating the molecular structures of the ligands with the predicted coordinative properties, generated a ranking list of potential compounds for Cs/Sr selective crystallization. The Sr2+ sequestration capability and selectivity over Cs+ of the promising ligands identified (squaric acid and chloranilic acid) were subsequently confirmed experimentally, with commendable performances, corroborating the artificial-intelligence-guided strategy.

Interactive Voice Response and Text-based Self-report Versions of the Electronic Columbia-Suicide Severity Rating Scale Are Equivalent.

Objectives: Our study objective was to compare the equivalence of a new version of the electronic Columbia-Suicide Severity Rating Scale that was administered on a tablet device with the existing interactive voice response version in order to support the prospective monitoring of suicidal ideation and behavior in clinical trials and clinical practice. Design: This was a randomized, crossover-equivalence study with no treatment intervention. Setting: The study setting was a psychiatric hospital. Participants: Fifty-eight recently admitted psychiatric inpatients and 28 employees of the hospital site were included in the study. Mean age was 41.0 years (standard deviation=12.5), and 59 percent were female. Measurements: Participants completed both tablet and interactive voice response versions in randomized order, with a 25-minute break between administrations. Finally, participants completed a second administration of the first administered version. Intraclass correlation coefficients (ICCs) and Kappa coefficients were used to evaluate agreement across modalities. Results: High levels of agreement were observed for most severe lifetime (ICC=0.88) and recent (ICC=0.79) ideation, occurrence of actual lifetime (Kappa=0.81) and recent (Kappa=0.73) suicide attempts, and occurrence of lifetime interrupted attempts (Kappa=0.78), aborted attempts (Kappa=0.54), and preparatory behaviors (Kappa=0.77), as well as non-suicidal self-injurious behavior (Kappa=0.73). Scores from both modes significantly differentiated psychiatric patients and hospital employee controls, and the test-retest reliability of both modes was excellent. Conclusions: These results support the validity and reliability of the new tablet-based electronic Columbia-Suicide Severity Rating Scale. This will allow the inclusion of the electronic Columbia-Suicide Severity Rating Scale in a wider range of clinical studies, particularly where a tablet is also being used to collect other study data.

Potential linkage between compound microsatellites and recombination in geminiviruses: Evidence from comparative analysis.

The compound microsatellites consist of two or more individual microsatellites, originate from mutation or imperfection in simple repeat sequences. The reports on systematic analysis of the occurrence, size and density of compound microsatellite (cSSR) types are very rare. Our study indicates that cSSRs are clustered at specific regions in the begomovirus genomes. cSSRs were overrepresented in majority of begomovirus genomes indicating that they might have some functional significance. Further, non-random distribution pattern of cSSR in begomovirus genomes was significantly correlated with the recombination breakpoint positions in the genome. The analysis of cSSR regions in the viral genome indicates the presence of stem loop (hairpin) secondary structure. The significance of these findings in biology of geminiviruses is discussed based on our present understanding of recombination and repetitive DNA. To our knowledge, this is the first analysis suggesting the possible association between recombination and microsatellites in any viral genome.

Genome-wide scan for analysis of simple and imperfect microsatellites in diverse carlaviruses.

An exhaustive compilation and analysis of incidence, distribution and variation of simple sequence repeats (SSRs) in viruses are required to understand the evolution and functional aspects of repetitive sequences. Present study focuses on the analysis of SSRs in 32 species of carlaviruses. The full length genome sequences were assessed from NCBI (http://www.ncbi.nlm.nih.-gov/) and analyzed using IMEx software. Variance in incidence of SSRs was observed, independent of genome size. Though the conversion of SSRs to imperfect microsatellite or compound SSR is low; compound microsatellites constituted by variant motifs accounted for up to 12.5% of the SSRs. Mononucleotide A/T is most prevalent followed by dinucleotide GT/TG and trinucleotide AAG/GAA in these genomes. The SSR and cSSR are predominantly localized to the coding region RDRP (RNA dependent RNA polymerase) and ORF-6 (open reading frame). The relative frequency of different classes of simple and compound microsatellites has been highlighted in accordance with the biology of carlavirus. Characterization of such variations would be pivotal for deciphering the enigma of these widely used, but incompletely understood sequences.

De novo assembly and characterization of the skeletal muscle and electric organ transcriptomes of the African weakly electric fish Campylomormyrus compressirostris (Mormyridae, Teleostei).

African weakly electric fishes (Mormyridae) underwent an outstanding adaptive radiation (about 200 species), putatively owing to their ability to communicate through species-specific weak electric signals. The electric organ discharge (EOD) is produced by muscle-derived electrocytes organized in piles to form an electric organ. Despite the importance of this trait as a prezygotic isolation mechanism, genomic resources remained limited. We present here a first draft of the skeletal muscle and electric organ transcriptomes from the weakly electric fish species Campylomormyrus compressirostris, obtained using the Illumina HiSeq2000 sequencing technology. Approximately 6.8 Gbp of cDNA sequence data were produced from both tissues, resulting in 57,268,109 raw reads for the skeletal muscle and 46,934,923 for the electric organ, and assembled de novo into 46,143 and 89,270 contigs, respectively. About 50% of both transcriptomes were annotated after protein databases search. The two transcriptomes show similar profiles in terms of Gene Ontology categories composition. We identified several candidate genes which are likely to play a central role in the production and evolution of the electric signal. For most of these genes, and for many other housekeeping genes, we were able to obtain the complete or partial coding DNA sequences (CDS), which can be used for the development of primers to be utilized in qRT-PCR experiments. We present also the complete mitochondrial genome and compare it to those available from other weakly electric fish species. Additionally, we located 1671 SSR-containing regions with their flanking sites and designed the relative primers. This study establishes a first step in the development of genomic tools aimed at understanding the role of electric communication during speciation.

Incidence, complexity and diversity of simple sequence repeats across potexvirus genomes.

An in-silico analysis of simple sequence repeats (SSRs) in genomes of 32 species of potexviruses was performed wherein a total of 691 SSRs and 33 cSSRs were observed. Though SSRs were present in all the studied genomes their incident frequency ranged from 11 to 30 per genome. Further, 10 potexvirus genomes possessed no cSSRs when extracted at a dMAX of 10 and wherein present, the highest frequency was 3. SSR and cSSR incidence, relative density and relative abundance were non-significantly correlated with genome size and GC content suggesting an ongoing evolutionary and adaptive phase of the virus species. SSRs present primarily ranged from mono- to tri-nucleotide repeat motifs with a greatly skewed distribution across the coding and non-coding regions. Present work is an effort for the undergoing compilation and analysis of incidence, distribution and variation of the viral repeat sequences to understand their evolutionary and functional relevance.

In- silico exploration of thirty alphavirus genomes for analysis of the simple sequence repeats.

The compilation of simple sequence repeats (SSRs) in viruses and its analysis with reference to incidence, distribution and variation would be instrumental in understanding the functional and evolutionary aspects of repeat sequences. Present study encompasses the analysis of SSRs across 30 species of alphaviruses. The full length genome sequences, assessed from NCBI were used for extraction and analysis of repeat sequences using IMEx software. The repeats of different motif sizes (mono- to penta-nucleotide) observed therein exhibited variable incidence across the species. Expectedly, mononucleotide A/T was the most prevalent followed by dinucleotide AG/GA and trinucleotide AAG/GAA in these genomes. The conversion of SSRs to imperfect microsatellite or compound microsatellite (cSSR) is low. cSSR, primarily constituted by variant motifs accounted for up to 12.5% of the SSRs. Interestingly, seven species lacked cSSR in their genomes. However, the SSR and cSSR are predominantly localized to the coding region ORFs for non structural protein and structural proteins. The relative frequencies of different classes of simple and compound microsatellites within and across genomes have been highlighted.

In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes.

An in-silico analysis of simple sequence repeats (SSRs) in 30 species of tobamoviruses was done. SSRs (mono to hexa) were present with variant frequency across species. Compound microsatellites, primarily of variant motifs accounted for up to 11.43% of the SSRs. Motif duplications were observed for A, T, AT, and ACA repeats. (AG)-(TC) was the most prevalent SSR-couple. SSRs were differentially localized in the coding region with ~54% on the 128 kDa protein while 20.37% was exclusive to 186 kDa protein. Characterization of such variations is important for elucidating the origin, sequence variations, and structure of these widely used, but incompletely understood sequences.