Inter-rater and Intra-rater Reliability of the Videofluoroscopic Dysphagia Scale with the Standardized Protocol

This study aimed to develop a standardized protocol for the assessment of videofluoroscopic dysphagia scale (VDS) and to demonstrate the inter-rater and intra-rater reliability of the VDS by applying the new standard protocol. A standardized protocol for the VDS was developed by dysphagia experts, including the original developer. To identify the reliability of the VDS using the protocol, 60 patients who underwent videofluoroscopic swallowing study (VFSS) for various etiologies were recruited retrospectively from three tertiary medical centers. Ten randomly selected cases were duplicated to evaluate the intra-rater reliability. Six physicians evaluated the VFSS data sets. Intraclass correlation coefficients were calculated for inter-rater and intra-rater reliability of the VDS score, and Gwet's kappa values for each VDS item were calculated. The inter-rater and intra-rater reliability of the total VDS score was 0.966 and 0.896, respectively. Notably, the evaluators' experience did not appear to have a significant impact on the reliability (physiatrists: 0.933/0.869, residents: 0.922/0.922). The reliability was consistent across different centers and dysphagia etiologies. The inter-rater and intra-rater reliability of the oral and pharyngeal sub-scores were 0.953/0.861 and 0.958/0.907, respectively. The inter-rater agreement of individual items ranged from 0.456 to 0.929, and nine items demonstrated good to very good level of agreement. Assessment of dysphagia using the VDS with the standard protocol showed excellent inter-rater and intra-rater reliabilities regardless of the evaluator's experience, VFSS equipment, and dysphagia etiologies. The VDS can be a useful assessment scale in the quantitative analysis of dysphagia based on VFSS findings.

Genome-wide identification of the PFK gene family and their expression analysis in Quercus rubra

The glycolytic pathway involves phosphofructokinase (PFK), a rate-limiting enzyme that catalyzes the phosphorylation of fructose-6-phosphate. In plants, the two PFK members are ATP-dependent phosphofructokinase (PFK) and pyrophosphate-fructose-6-phosphate phosphotransferase (PFP). However, the functions of the PFK family members in Quercus rubra are not well understood. The purpose of this study was to investigate the genome-wide distribution of the PFK family members and their roles in Q. rubra by performing a systematic study of the phylogenetic relationships, molecular characteristics, motifs, chromosomal and subcellular locations, and cis-elements of QrPFKs. We identified 14 QrPFK genes in the genome of Q. rubra, followed by examining their expression in different tissues, including the roots, stems, and leaves. The phylogenetic tree divided the 14 QrPFK genes into two groups: 11 belonging to PFK and three belonging to PFP. The expression profiles of all 14 proteins were relatively the same in leaves but differed between stems and roots. Four genes (Qurub.02G189400.1, Qurub.02G189400.2, Qurub.09G134300.1, and Qurub.09G134300.2) were expressed at very low levels in both stems and roots, while two (Qurub.05G235500.1 and Qurub.05G235500.1) were expressed at low levels and the others showed relatively high expression in all tissues.

Transcriptomic and Physiological Analysis Reveals Genes Associated with Drought Stress Responses in Populus alba × Populus glandulosa

Drought stress affects plant productivity by altering plant responses at the morphological, physiological, and molecular levels. In this study, we identified physiological and genetic responses in Populus alba × Populus glandulosa hybrid clones 72-30 and 72-31 after 12 days of exposure to drought treatment. After 12 days of drought treatment, glucose, fructose, and sucrose levels were significantly increased in clone 72-30 under drought stress. The Fv/Fo and Fv/Fm values in both clones also decreased under drought stress. The changes in proline, malondialdehyde, and H2O2 levels were significant and more pronounced in clone 72-30 than in clone 72-31. The activities of antioxidant-related enzymes, such as catalase and ascorbate peroxidase, were significantly higher in the 72-31 clone. To identify drought-related genes, we conducted a transcriptomic analysis in P. alba × P. glandulosa leaves exposed to drought stress. We found 883 up-regulated and 305 down-regulated genes in the 72-30 clone and 279 and 303 in the 72-31 clone, respectively. These differentially expressed genes were mainly in synthetic pathways related to proline, abscisic acid, and antioxidants. Overall, clone 72-31 showed better drought tolerance than clone 72-30 under drought stress, and genetic changes also showed different patterns.

Cardiopulmonary Response to Robot-Assisted Tilt Table With Regard to Its Components

Cardiopulmonary function is exceptionally critical during the early stages of rehabilitation after neurological disorders such as stroke, spinal cord injury and Parkinson's disease. This study aimed to demonstrate how robot-assisted and tilt table exercises affect cardiopulmonary function. In this study, ten healthy young adults performed six combinations of conditions according to robot-assisted mode (on/off), angle of tilt table (20°/60°), and functional electrical stimulation (FES) mode (on/off). Four conditions had FES mode off with combinations of robot-assisted mode (on/off) and tilt angle (20°/60°) and two conditions had robot-assisted mode and FES on with tilt angle (20°/60°). Cardiopulmonary effects (oxygen uptake [VO₂], peak oxygen uptake [VO₂peak], metabolic energy cost [MET], rate pressure product [RPP], heart rate [HR], maximum heart rate [%HRmax], and minute ventilation [VE]) were compared in each condition. As a result, in the angle and FES mode effect, VO₂, VO₂peak, MET, RPP, HR, and %HRmax, unlike that for VE, showed major effects in angle. In addition, in the robot-assisted mode and angle effect, when the FES was switched off, VO₂, METs, and VE values showed major effects in the robot-assisted mode, whereas all other values showed major effects in angle. Compared to earlier reported findings, we can expect that robot-assisted tilt table training can lead to changes in the cardiopulmonary function.

Elevated CO2 Alters the Physiological and Transcriptome Responses of Pinus densiflora to Long-Term CO2 Exposure

Physiological response and transcriptome changes were observed to investigate the effects on the growth, metabolism and genetic changes of Pinus densiflora grown for a long time in an environment with an elevated atmospheric CO₂ concentration. Pine trees were grown at ambient (400 ppm) and elevated (560 ppm and 720 ppm) CO₂ concentrations for 10 years in open-top chambers. The content of nonstructural carbohydrates was significantly increased in elevated CO₂. It was notable that the contents of chlorophylls significantly decreased at an elevated CO₂. The activities of antioxidants were significantly increased at an elevated CO₂ concentration of 720 ppm. We analyzed the differences in the transcriptomes of Pinus densiflora at ambient and elevated CO₂ concentrations and elucidated the functions of the differentially expressed genes (DEGs). RNA-Seq analysis identified 2415 and 4462 DEGs between an ambient and elevated CO₂ concentrations of 560 ppm and 720 ppm, respectively. Genes related to glycolysis/gluconeogenesis and starch/sucrose metabolism were unchanged or decreased at an elevated CO₂ concentration of 560 ppm and tended to increase at an elevated CO₂ concentration of 720 ppm. It was confirmed that the expression levels of genes related to photosynthesis and antioxidants were increased at an elevated CO₂ concentration of 720 ppm.

Fracture risk and impact of osteoporosis in patients with Parkinson's disease: a nationwide database study

INTRODUCTION

Patients with Parkinson's disease (PD) showed an increased risk of fractures in previous studies and a high prevalence of osteoporosis is reportedly a potential contributor. We conducted a nationwide database study on the risk of fractures and the impact of osteoporosis on patients with PD compared to controls.

MATERIALS AND METHODS

Using a nationwide database in South Korea, we identified incident patients with PD in 2004-2006 and selected four age- and sex-matched controls. We checked the occurrence rates of overall and hip fractures and plotted Kaplan-Meier curves and a Cox proportional hazards model to determine risk. We also conducted stratified analyses according to the presence or absence of osteoporosis.

RESULTS

We identified 9126 patients with PD and 35,601 controls. Patients with PD had a greater probability of fractures throughout the study period in Kaplan-Meier curves, and an increased risk of overall (aHR 1.35, 95% CI 1.297-1.405) and hip (aHR 1.814, 95% CI 1.66-1.983) fractures in a Cox proportional hazards model. In the stratified analysis, the increased risk of overall fracture (aHR 1.333, 95% CI 1.273-1.396 and aHR 1.412, 95% CI 1.301-1.532, respectively) and hip fracture (aHR 1.773, 95% CI 1.604-1.96 and aHR 2.008, 95% CI 1.657-2.434, respectively) due to PD was similar between patients with and without osteoporosis.

DISCUSSION

Patients with PD, with or without osteoporosis, are more likely to experience fractures, especially hip fractures. There seems to be no interaction between PD and osteoporosis in regard to the occurrence of fractures, and therefore no effect modification by osteoporosis.

The Korean Version of the Fugl-Meyer Assessment: Reliability and Validity Evaluation

Objective

To systematically translate the Fugl-Meyer Assessment (FMA) into a Korean version of the FMA (K-FMA).

Methods

We translated the original FMA into the Korean version with three translators and a translation committee, which included physiatrists, physical therapists, and occupational therapists. Based on a test-retest method, each of 31 patients with stroke was assessed by two evaluators twice, once on recruitment, and again after a week. Analysis of intra- and inter-rater reliabilities was performed using the intra-class correlation coefficient, whereas validity was analysed using Pearson correlation test along with the Motricity Index (MI), Motor Assessment Scale (MAS), and Berg Balance Scale (BBS).

Results

The intra- and inter-rater reliabilities were significant for the total score, and good to excellent reliability was noted in all domains except for the joint range of motion of the lower extremity domain of the K-FMA. The MI and MAS scores were significantly correlated with all domains, all with p<0.01. The results for the MI ranged from r=0.639 to r=0.891 and those for the MAS from r=0.339 to r=0.555. However, the BBS was not significantly correlated with any domain, as the K-FMA lacks balance evaluation items.

Conclusion

The K-FMA was found to have high reliability and validity. Additionally, the newly developed manual for the K-FMA may help minimise errors that can occur during evaluation and improve the reliability of motor function evaluation.

FOPR test: a virtual reality-based technique to assess field of perception and field of regard in hemispatial neglect

BACKGROUND

We previously proposed a novel virtual reality-based method to assess human field of perception (FOP) and field of regard (FOR), termed the FOPR test. This study assessed the diagnostic validity of the FOPR test for hemispatial neglect (HSN).

METHODS

We included 19 stroke patients with a lesion in the right hemisphere and with HSN (HSN+SS), 22 stroke patients with a lesion in the right hemisphere and without HSN (HSN-SS), and 22 healthy controls aged 19-65 years. The success rate (SR) and response time (RT) in the FOPR test for both FOP and FOR were assessed (FOP-SR, FOR-SR, FOP-RT, and FOR-RT, respectively). Using a Bland-Altman plot, agreements between the FOPR test and conventional tests were confirmed, and the FOPR test accuracy was verified using the support vector machine (SVM). Measured values were analysed using ANOVA and Kruskall-Wallis tests for group comparison.

RESULTS

The Bland-Altman plot showed good agreement between FOPR test and conventional tests; individuals within 95% agreement limits were within the range of 94.8-100.0%. The SVM classification accuracy, using FOP and FOR variables from the left hemispace, ranged from 83.3 to 100.0% in a binary classification (HSN vs non-HSN). The FOPR test demonstrated differences in SR and RT for both FOP and FOR across the groups.

CONCLUSION

The FOPR test was valid for the HSN diagnosis and provided quantitative and intuitive information regarding visuospatial function. Furthermore, it might enhance our understanding of visuospatial function including HSN by applying the time relative component and concepts of perception and exploration, FOP and FOR.

TRIAL REGISTRATION

NCT03463122. Registered 13 March 2018, retrospectively registered.

Fine Mutational Analysis of 2B8 and 3H7 Tag Epitopes with Corresponding Specific Monoclonal Antibodies

Bacteriophytochromes are phytochrome-like light-sensing photoreceptors that use biliverdin as a chromophore. To study the biochemical properties of the Deinococcus radiodurans bacteriophytochrome (DrBphP) protein, two anti-DrBphP mouse monoclonal antibodies (2B8 and 3H7) were generated. Their specific epitopes were identified in our previous report. We present here fine epitope mapping of these two antibodies by using truncation and substitution of original epitope sequences in order to identify minimized epitope peptides. The previously reported original epitope sequences for 2B8 and 3H7 were truncated from both sides. Our analysis showed that the minimal peptide sequence lengths for 2B8 and 3H7 antibodies were nine amino acids (RDPLPFFPP) and six amino acids (PGEIEE), respectively. We further characterized these peptides in order to investigate their reactivity after single deletion and single substitution of the original peptides. We found that single-substituted 2B8 epitope (RDPLPAFPP) and dual-substituted 3H7 epitope (PGEIAD) showed significantly increased reactivity. These two antibodies with high reactivity for the short modified peptide sequences are valueble for developing new peptide tags for protein research.

Epitope mapping of monoclonal antibodies for the Deinococcus radiodurans bacteriophytochome

Bacteriophytochromes (BphP) are phytochrome-like light sensing proteins in bacteria, which use biliverdin as a chromophore. In order to study the biochemical properties of the DrBphP protein, five (2B8, 2C11, 3B2, 3D2, and 3H7) anti-DrBphP monoclonal antibodies were produced through the immunization of mice with purified full-length DrBphP and DrBphN (1-321 amino acid) proteins, and epitope mapping was then carried out. Among the five antibodies, 2B8 and 2C11 preferentially recognized the N-terminal region of BphP whereas 3B2, 3D2, and 3H7 showed preference for the C-terminal region. We performed further epitope mapping using recombinant truncated BphP proteins to narrow down their target sequences. The results demonstrated that each of the five monoclonal antibodies recognized different regions on the DrBphP protein. Additionally, epitopes of 2B8 and 3H7 antibodies were discovered to be shorter than 10 amino acids (2B8: RDPLPFFPP, 3H7: PGEIEEA). These two antibodies with such specific recognition epitopes could be especially valuable for developing new peptide tags for protein detection and purification.

An ankyrin repeat protein is involved in anthocyanin biosynthesis in Arabidopsis

The ankyrin domain is one of the most common protein motifs in eukaryotic proteins. Repeated ankyrin domains are ubiquitous and their mediation of protein-protein interactions is involved in a number of physiological and developmental responses such as the cell cycle, signal transduction and cell differentiation. A novel putative phytochrome-interacting ankyrin repeat protein 2 (PIA2) containing three repeated ankyrin domains was identified in Arabidopsis. An in vitro pull-down and phosphorylation assay revealed that PIA2 is phosphorylated and interacts directly with oat phytochrome A. The N-terminal domain of PIA2 was specifically phosphorylated, whereas interactions between the domains of PIA2 and phytochrome A had no Pr/Pfr preference. PIA2 was ubiquitously expressed in most tissues and was localized in both the nucleus and the cytoplasm independent of treatment with light of specific wavelengths. Anthocyanin accumulation in seedlings grown under far-red light, a typical phenotype of wild-type plants, was reduced in a loss-of-function mutant of PIA2 (pia2), whereas anthocyanin accumulation was increased in an overexpressing plant (PIA2-OX). The gene expression of UDP-flavonoid-3'-glucosyl-transferase (UF3GT), a major enzyme in the anthocyanin biosynthesis processes, was decreased in pia2 knockout plants suggesting that decreased anthocyanin was because of the decreased expression of UF3GT. Our results suggest that PIA2 plays a role in the anthocyanin biosynthesis during seedling development as a novel phytochrome-interacting protein.

A small GTPase activator protein interacts with cytoplasmic phytochromes in regulating root development

Phytochromes enable plants to sense light information and regulate developmental responses. Phytochromes interact with partner proteins to transmit light signals to downstream components for plant development. PIRF1 (phytochrome-interacting ROP guanine-nucleotide exchange factor (RopGEF 1)) functions as a light-signaling switch regulating root development through the activation of ROPs (Rho-like GTPase of plant) in the cytoplasm. In vitro pulldown and yeast two-hybrid assays confirmed the interaction between PIRF1 and phytochromes. PIRF1 interacted with the N-terminal domain of phytochromes through its conserved PRONE (plant-specific ROP nucleotide exchanger) region. PIRF1 also interacted with ROPs and activated them in a phytochrome-dependent manner. The Pr form of phytochrome A enhanced the RopGEF activity of PIRF1, whereas the Pfr form inhibited it. A bimolecular fluorescence complementation analysis demonstrated that PIRF1 was localized in the cytoplasm and bound to the phytochromes in darkness but not in light. PIRF1 loss of function mutants (pirf1) of Arabidopsis thaliana showed a longer root phenotype in the dark. In addition, both PIRF1 overexpression mutants (PIRF1-OX) and phytochrome-null mutants (phyA-211 and phyB-9) showed retarded root elongation and irregular root hair formation, suggesting that PIRF1 is a negative regulator of phytochrome-mediated primary root development. We propose that phytochrome and ROP signaling are interconnected through PIRF1 in regulating the root growth and development in Arabidopsis.

Polyamine depletion partially reduces the radiation-induced cell death via cell cycle delay mediated by thioredoxin

In previous studies, polyamine depletion by DFMO (alpha-difluoromethylornithine)-treatment reduced H(2)O(2)-induced apoptotic cell death by reduction of ferric ion uptake. In the present study, we analyzed the reduction of radiation-induced cell death by polyamine depletion. Exposure of HT29 cells to radiation induced severe cell death, but when cells were pretreated with DFMO, a specific inhibitor of polyamine biosynthesis, radiation-induced cell death was reduced to 50-60% of control. Cell cycle analysis showed that, in these cells, the time to reach the G(2)/M phase arrest was delayed for 20-24 h compared to the control cells, at which stage the fate of cells exposed to ionizing radiation is determined. DFMO-treated cells also showed a low level of thioredoxin, which is a high-level determinant of the cellular fate. To investigate the relationship between the G(2)/M phase arrest and the reduction of thioredoxin caused by polyamine depletion, we also analyzed thioredoxin-antisensed (asTRX) HT29 cells as for DFMO-treated cells. In asTRX-transfected cells, the gamma-irradiation-induced G(2)/M phase arrest was also significantly delayed and radiation-induced cell death was profoundly reduced, as in the DFMO-treated cells. Both sets of cells showed a decrease of cyclin D1 and an increment of HSP25, which are involved in radiation-induced cell cycle progress. Overall, these results suggest that polyamines are essential for normal cell death of HT29 cells triggered by gamma-radiation and that this is partially mediated by the regulation of thioredoxin expression.

Two-loop calculation of the turbulent Prandtl number

The turbulent Prandtl number has been calculated in the two-loop approximation of the epsilon expansion of the stochastic theory of turbulence. The strikingly small value obtained for the two-loop correction explains the good agreement of the earlier one-loop result with the experiment. This situation is drastically different from other available nontrivial two-loop results, which exhibit corrections of the magnitude of the one-loop term. The reason is traced to the mutual cancellation of additional divergences appearing in two dimensions, which have had a major effect on the results of previous calculations of other quantities.

Anomalous scaling of a passive scalar advected by the Navier-Stokes velocity field: two-loop approximation

The field theoretic renormalization group and operator-product expansion are applied to the model of a passive scalar quantity advected by a non-Gaussian velocity field with finite correlation time. The velocity is governed by the Navier-Stokes equation, subject to an external random stirring force with the correlation function proportional to delta(t- t')k(4-d-2epsilon). It is shown that the scalar field is intermittent already for small epsilon, its structure functions display anomalous scaling behavior, and the corresponding exponents can be systematically calculated as series in epsilon. The practical calculation is accomplished to order epsilon2 (two-loop approximation), including anisotropic sectors. As for the well-known Kraichnan rapid-change model, the anomalous scaling results from the existence in the model of composite fields (operators) with negative scaling dimensions, identified with the anomalous exponents. Thus the mechanism of the origin of anomalous scaling appears similar for the Gaussian model with zero correlation time and the non-Gaussian model with finite correlation time. It should be emphasized that, in contrast to Gaussian velocity ensembles with finite correlation time, the model and the perturbation theory discussed here are manifestly Galilean covariant. The relevance of these results for real passive advection and comparison with the Gaussian models and experiments are briefly discussed.