Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology

Seed shape is an important agronomic trait with continuous variation among genotypes. Therefore, the quantitative evaluation of this variation is highly important. Among geometric morphometrics methods, elliptic Fourier analysis and semi-landmark analysis are often used for the quantification of biological shape variations. Elliptic Fourier analysis is an approximation method to treat contours as a waveform. Semi-landmark analysis is a method of superimposed points in which the differences of multiple contour positions are minimized. However, no detailed comparison of these methods has been undertaken. Moreover, these shape descriptors vary when the scale and direction of the contour and the starting point of the contour trace change. Thus, these methods should be compared with respect to the standardization of the scale and direction of the contour and the starting point of the contour trace. In the present study, we evaluated seed shape variations in a sorghum (Sorghum bicolor Moench) germplasm collection to analyze the association between shape variations and genome-wide single-nucleotide polymorphisms by genomic prediction (GP) and genome-wide association studies (GWAS). In our analysis, we used all possible combinations of three shape description methods and eight standardization procedures for the scale and direction of the contour as well as the starting point of the contour trace; these combinations were compared in terms of GP accuracy and the GWAS results. We compared the shape description methods (elliptic Fourier descriptors and the coordinates of superposed pseudo-landmark points) and found that principal component analysis of their quantitative descriptors yielded similar results. Different scaling and direction standardization procedures caused differences in the principal component scores, average shape, and the results of GP and GWAS.

Methotrexate-related lymphoproliferative disorders in the liver: Case presentation and mini-review

BACKGROUND

Immunosuppression is effective in treating a number of diseases, but adverse effects such as bone marrow suppression, infection, and oncogenesis are of concern. Methotrexate is a key immunosuppressant used to treat rheumatoid arthritis. Although it is effective for many patients, various side effects have been reported, one of the most serious being methotrexate-related lymphoproliferative disorder. While this may occur in various organs, liver involvement is rare. Information on these liver lesions, including clinical characteristics, course, and imaging studies, has not been summarized to date.

CASE SUMMARY

We present a case of 70-year-old woman presented with a 2-wk history of fever and abdominal pain. She had had rheumatoid arthritis for 5 years and was being treated with medication including methotrexate. Contrast-enhanced computed tomography revealed multiple low density tumors in the liver and the histological analyses showed significant proliferation of lymphocytes in masses that were positive on immunohistochemical staining for CD3, CD4, CD8, and CD79a but negative for CD20 and CD56. Staining for Epstein-Barr virus-encoded RNA was negative. And based on these findings, the liver tumors were diagnosed as Methotrexate-related lymphoproliferative disorders. A time-dependent disappearance of the liver tumors after stopping methotrexate supported the diagnoses.

CONCLUSION

The information obtained from our case and a review of 9 additional cases reported thus far assist physicians who may face the challenge of diagnosing and managing this disorder.

Enterovirus-Associated Hand-Foot and Mouth Disease and Neurological Complications in Japan and the Rest of the World

Enteroviruses (EVs) are responsible for extremely large-scale, periodic epidemics in pediatric cohorts, particularly in East and Southeast Asia. Clinical presentation includes a diverse disease spectrum, including hand-foot and mouth disease (HFMD), aseptic meningitis, encephalitis, acute flaccid paralysis, and acute flaccid myelitis. HFMD is predominantly attributable to EV-A types, including the major pathogen EV-A71, and coxsackieviruses, particularly CV-A6, CV-A16, and CV-A10. There have been multiple EV-A71 outbreaks associated with a profound burden of neurological disease and fatal outcomes in Asia since the early 1980s. Efficacious vaccines against EV-A71 have been developed in China but widespread pediatric vaccination programs have not been introduced in other countries. Encephalitis, as a consequence of complications arising from HFMD infection, leads to damage to the thalamus and medulla oblongata. Studies in Vietnam suggest that myoclonus is a significant indicator of central nervous system (CNS) complications in EV-A71-associated HFMD cases. Rapid response in HFMD cases in children is imperative to prevent the progression to a CNS infection; however, prophylactic and therapeutic agents have not been well established internationally, therefore surveillance and functional studies including development of antivirals and multivalent vaccines is critically important to reduce disease burden in pediatric populations.

Altered expression of long noncoding RNAs in patients with major depressive disorder

Although major depressive disorder (MDD) is a leading cause of disability worldwide, its pathophysiology is poorly understood. Increasing evidence suggests that aberrant regulation of transcription plays a key role in the pathophysiology of MDD. Recently, long noncoding RNAs (lncRNAs) have been recognized for their important functions in chromatin structure, gene expression, and the subsequent manifestation of various biological processes in the central nervous system. However, it is unclear whether the aberrant expression and function of lncRNAs are associated with the pathophysiology of MDD. In this study, we sought to evaluate the expression of lncRNAs in peripheral blood leukocytes as potential biomarkers for MDD. We measured the expression levels of 83 lncRNAs in the peripheral blood leukocytes of 29 MDD patients and 29 age- and gender-matched healthy controls using quantitative reverse transcription PCR (RT-qPCR) analysis. We found that MDD patients exhibited distinct expression signatures. Specifically, the expression level of one lncRNA (RMRP) was lower while the levels of four (Y5, MER11C, PCAT1, and PCAT29) were higher in MDD patients compared to healthy controls. The expression level of RMRP was correlated with depression severity as measured by the Hamilton Depression Rating Scale (HAM-D). Moreover, RMRP expression was lower in a mouse model of depression, corroborating the observation from MDD patients. Taken together, our data suggest that lower RMRP levels may serve as a potential biomarker for MDD.

P2696Clinical characteristics of late catch-up phenomenon after implantation of 2nd generation drug eluting stent

Introduction

Late catch-up phenomenon (LCU) of 1st generation drug eluting stent (DES) has been increasing yearly despite the rate of restenosis in 1 year has reduced compared with bare metal stent (BMS). 2nd generation DES was more improved than 1st generation DES and suggested more benefits about clinical outcome.

Purpose

To investigate the incidence and predictor of LCU after implantation of 2nd generation DES and to evaluate the association between LCU phenomenon and adverse events.

Methods

Between August 2012 and July 2013, a total of 1665 consecutive patients (1956 lesions with elective/urgent PCI) were enrolled in SHINANO 5 years Registry (a prospective observational multicenter cohort study) from 13 institutions in Nagano, Japan. 711 patients that were treated with 2nd generation DES and 576 patients with BMS were selected. Exclusion criterias were cases of 1st DES, only POBA, only aspiration and chronic total occulusion.

Results

There were significant difference about patients background between BMS and 2nd generation DES groups. Those groups were matched with propensity score. After matching, 822 patients (BMS group 411 patients, 2nd generation group 411 patients) were analyzed. The rates of 2nd DES and BMS restenosis 5 years after initial PCI were 9.2% and 8.5% (p=0.572), those of LCU were 2.6% and 5.6% (p=0.043) by 1 year landmark analysis. Cox proportional hazards analysis revealed that the DES in-stent restenosis (ISR) lesion and higher HbA1c were independent predictors for LCU from 1year to 5year (HR 5.304, p=0.009, HR 1.254, p=0.015), but 2nd generation DES was not. Kaplan Meier curve showed no association between LCU phenomenon and all cause death (p=0.446). Cox regression analysis showed LCU was not independent predictor for all cause death (p=0.414).

Conclusions

Implantation to DES-ISR lesion with 2nd generation DES was associated with higher LCU. Despite of more complex lesions with 2nd generation DES, there were no differences of LCU incidence between 2nd generation DES and BMS.

Acknowledgement/Funding

None

Measurements of radial profile of hydrogen and deuterium density in isotope mixture plasmas using bulk charge exchange spectroscopy

A bulk charge exchange spectroscopy system has been applied to measure the radial profiles of the hydrogen (H) and deuterium (D) density ratio in the isotope mixture plasma in a large helical device. Charge exchange lines of H_α and D_α are fitted by 4 Gaussian of H and D cold components and H and D hot components with 5 parameters by combining the measurement of plasma toroidal rotation velocity with carbon charge exchange spectroscopy. The radial profiles of the relative density of hydrogen and deuterium ions are derived from H and D hot components measured and the beam density calculated from beam attenuation calculation. A proof-of-principle experiment is performed by the H pellet and the D pellet injections into the H-D mixture plasma.

Determining effectiveness of rotavirus vaccine by immunochromatography and reverse transcriptase polymerase chain reaction: A comparison

INTRODUCTION

Because of the large animal reservoirs and reassortment capacity of rotaviruses (RVs) that pose the possibilities of waning the effectiveness of RV-vaccines, it remains essential to monitor vaccine effectiveness (VE) regularly. Although reverse transcription polymerase chain reaction (RT-PCR) remains sensitive for RV detection, physicians, especially in Japan, frequently use immunochromatography (IC)-based kits for RV diagnosis. Recently, IC is being used to calculate VE also. Herein, we investigated the validity of VEs determined by IC compared to that by RT-PCR during an outbreak in Shizuoka Prefecture, Japan.

METHODS

RVs in the stool or rectal swabs from children with acute gastroenteritis (AGE) were tested first by IC in the clinic and then by RT-PCR in the laboratory. A test-negative study design was used to examine VE.

RESULTS

Although the specificity of IC assay revealed 100%, its sensitivity remained weaker (67%) than that of RT-PCR that increased up to 88% depending on disease severity. VE assessed by IC remained stronger than that by RT-PCR: 79% (95% CI: 39-93%) by IC, and 58% (95% CI: -20% to 90%) by RT-PCR. However, VEs by IC and RT-PCR appeared almost similar in higher disease severity: 81.5% (95% CI: 40-94%) by IC and 72% (95% CI: 7-92%) by RT-PCR at severity ≥7, while 97.5% (95% CI: 77-99.7%) by IC and 92% (95% CI: 58-98%) by RT-PCR at severity ≥11. We showed that RV-vaccinated children had 80% [OR = 0.192 (95% CI: 0.052-0.709) less chance to be detected by IC.

CONCLUSION

Although the sensitivity and specificity of IC differ by brand type, generally, IC is not as sensitive as RT-PCR. Despite the VEs remain higher by IC, it looks comparable with that of RT-PCR in severe cases implying that VEs evaluated by IC against severe illness remain useful for VE-monitoring.

Evaluating the effect of injecting triamcinolone acetonide in two sessions for preventing esophageal stricture after endoscopic submucosal dissection

Background and study aims  Several previous reports indicate that endoscopic injection of triamcinolone acetonide (TA) after widespread endoscopic submucosal dissection (ESD) is effective for preventing esophageal stricture. We investigated the efficacy of injecting TA in two sessions for preventing stricture formation post-ESD. Patients and methods  Sixty-six consecutive patients with widespread mucosal defects that affected more than three-fourths of the circumference of the esophagus were included. The study group (n = 40) received TA injections over two sessions: immediately after and 14 days after ESD. The control group (n = 26) did not receive a TA injection. This study was performed retrospectively against historical controls. The primary endpoint of this study was frequency of stricture after TA injection. The secondary endpoint was number of required endoscopic balloon dilations (EBDs) after TA injection. Results  The post-ESD stricture rate among patients who had subcircumferential mucosal defects was 45.7 % in the study group (16/35 patients), which was significantly lower than the rate of 73.9 % in the control group (17/23 patients; P  = 0.031). The number of EBD procedures required was significantly lower in the study group (median 0, range 0 - 7) than in the control group (median 4, range 0 - 20; P  < 0.001). There was no significant difference between the study and control groups among the patients who had full circumferential mucosal defects. Conclusion  This study showed that performing two sessions of TA injection is an effective and safe treatment for prevention of esophageal stricture following subcircumferential ESD.

Longitudinal changes in 18 F-THK5351 positron emission tomography in corticobasal syndrome

BACKGROUND AND PURPOSE

Corticobasal syndrome (CBS) is pathologically characterized by tau deposits in neuronal and glial cells and by reactive astrogliosis. In several neurodegenerative disorders, ¹⁸ F-THK5351 has been observed to bind to reactive astrocytes expressing monoamine oxidase B. In this study, the aim was to investigate the progression of disease-related pathology in the brains of patients with CBS using positron emission tomography with ¹⁸ F-THK5351.

METHODS

Baseline and 1-year follow-up imaging were acquired using magnetic resonance imaging and positron emission tomography with ¹⁸ F-THK5351 in 10 subjects: five patients with CBS and five age-matched normal controls (NCs).

RESULTS

The 1-year follow-up scan images revealed that ¹⁸ F-THK5351 retention had significantly increased in the superior parietal gyrus of the patients with CBS compared with the NCs. The median increases in ¹⁸ F-THK5351 accumulation in the patients with CBS were 6.53% in the superior parietal gyrus, 4.34% in the precentral gyrus and 4.33% in the postcentral gyrus. In contrast, there was no significant increase in the regional ¹⁸ F-THK5351 retention in the NCs.

CONCLUSIONS

Longitudinal increases in ¹⁸ F-THK5351 binding can be detected over a short interval in the cortical sites of patients with CBS. A monoamine oxidase B binding radiotracer could be useful in monitoring the progression of astrogliosis in CBS.

GPR34 in spinal microglia exacerbates neuropathic pain in mice

Background

Neuropathic pain is caused by sensory nerve injury, but effective treatments are currently lacking. Microglia are activated in the spinal dorsal horn after sensory nerve injury and contribute to neuropathic pain. Accordingly, molecules expressed by these cells are considered potential targets for therapeutic strategies. Our previous gene screening study using a mouse model of motor nerve injury showed that the G-protein-coupled receptor 34 gene (GPR34) is induced by nerve injury. Because GPR34 is now considered a microglia-enriched gene, we explored the possibility that it might be involved in microglial activation in the dorsal horn in a mouse model of neuropathic pain.

Methods

mRNA expression of GPR34 and pro-inflammatory molecules was determined by quantitative real-time PCR in wild-type and GPR34-deficient mice with L4 spinal nerve injury. In situ hybridization was used to identify GPR34 expression in microglia, and immunohistochemistry with the microglial marker Iba1 was performed to examine microglial numbers and morphology. Mechanical sensitivity was evaluated by the von Frey hair test. Liquid chromatography–tandem mass spectrometry quantified expression of the ligand for GPR34, lysophosphatidylserine (LysoPS), in the dorsal horn, and a GPR34 antagonist was intrathecally administrated to examine the effect of inhibiting LysoPS-GPR34 signaling on mechanical sensitivity.

Results

GPR34 was predominantly expressed by microglia in the dorsal horn after L4 nerve injury. There were no histological differences in microglial numbers or morphology between WT and GPR34-deficient mice. However, nerve injury-induced pro-inflammatory cytokine expression levels in microglia and pain behaviors were significantly attenuated in GPR34-deficient mice. Furthermore, the intrathecal administration of the GPR34 antagonist reduced neuropathic pain.

Conclusions

Inhibition of GPR34-mediated signal by GPR34 gene deletion reduced nerve injury-induced neuropathic pain by suppressing pro-inflammatory responses of microglia without affecting their morphology. Therefore, the suppression of GPR34 activity may have therapeutic potential for alleviating neuropathic pain.

Electronic supplementary material

The online version of this article (10.1186/s12974-019-1458-8) contains supplementary material, which is available to authorized users.

Expression of Genes from Paternal Alleles in Rice Zygotes and Involvement of OsASGR-BBML1 in Initiation of Zygotic Development

Upon fertilization in angiosperms, one sperm cell fuses with the egg cell to produce a zygote, and, via karyogamy, the parental genetic information is combined to form the diploid zygotic genome. Recently, analyses with parentally imbalanced rice zygotes indicated that parental genomes are utilized synergistically in zygotes with different functions, and that genes transcribed from the paternal or maternal allele might play important roles in zygotic development. Herein, we first conducted single nucleotide polymorphism-based mRNA-sequencing using intersubspecific rice zygotes. Twenty-three genes, with paternal allele-specific expression in zygotes, were identified, and, surprisingly, their allele dependencies in the globular-like embryo tended to be biallelic. This suggests that the paternal-dependent expression of these genes is temporary, occurring during the early stages of zygote development. Of the 23 genes, we focused on Oryza sativa Apospory-specific Genome Region (ASGR)-BABY-BOOM LIKE (BBML) 1 (OsASGR-BBML1), presumed to encode an AP2-transcription factor, due to its reported role in zygotic development. Interestingly, ectopic expression of OsASGR-BBML1 in egg cells induced nuclear and cell divisions, indicating that exogenously expressed OsASGR-BBML1 converts the proliferation status of the egg cell from quiescent to active. In addition, the suppression of the function of OsASGR-BBML1 and its homologs in zygotes resulted in the developmental arrest, suggesting that OsASGR-BBML1 possesses an important role in initiating zygotic development. Monoallelic or preferential gene expression from the paternal genome in the zygote might be a safety mechanism allowing egg cells to suppress the gene expression cascade toward early embryogenesis that is normally triggered by fusion with a sperm cell.

Entirely Suprasellar Rathke Cleft Cysts: Clinical Features and Surgical Efficacy of Endoscopic Endonasal Transtuberculum Sellae Approach

BACKGROUND

Rathke cleft cysts (RCCs) arise from the remnant of Rathke pouch and are usually found in the intermediate lobe. In most cases, RCCs remain intrasellar and extend into the suprasellar region. Rarely, they emerge entirely into the suprasellar cistern-entirely suprasellar Rathke cleft cyst (ESSRCC).

METHODS

We retrospectively reviewed medical records of 7 patients (5.5%) with ESSRCC among 128 patients with a diagnosis of RCC from January 1994 to September 2018. Of RCC cases, 70 were treated surgically. Patient age and sex, symptoms, magnetic resonance imaging findings, cyst diameter, presence of preoperative or postoperative hypopituitarism, operative procedures and complications, and functional outcomes at the final follow-up were investigated.

RESULTS

All patients with ESSRCC were women with mean age 45.7 years (range, 29-69 years) at diagnosis. All patients experienced headache, mainly in the retro-orbital region. Mean ESSRCC diameter was 9.9 mm (range, 6-14 mm). Most cases exhibited hyperintensity on both T1-weighted and T2-weighted imaging. The endoscopic endonasal transtuberculum sellae approach relieved headache effectively and safely in 5 patients. Postoperative endocrinologic functions were almost entirely preserved. No patient experienced recurrence during the follow-up period.

CONCLUSIONS

RCCs should be considered in the differential diagnosis of suprasellar cysts. The endoscopic endonasal transtuberculum sellae approach has an advantage in visualizing these lesions owing to the direction of light from the endoscope. Headache could be treated effectively with the endoscopic endonasal transtuberculum sellae approach without recurrence of cysts or pituitary dysfunction.

First Measurement of a Long-Lived π^{+}π^{-} Atom Lifetime

The adapted DIRAC experiment at the CERN PS accelerator observed for the first time long-lived hydrogenlike π^{+}π^{-} atoms, produced by protons hitting a beryllium target. A part of these atoms crossed the gap of 96 mm between the target and a 2.1  μm thick platinum foil, in which most of them dissociated. Analyzing the observed number of atomic pairs, n_{A}^{L}=436_{-61}^{+157}|_{tot}, the lifetime of the 2p state is found to be τ_{2p}=(0.45_{-0.30}^{+1.08}|_{tot})×10^{-11}  s, not contradicting the corresponding QED 2p state lifetime τ_{2p}^{QED}=1.17×10^{-11}  s. This lifetime value is three orders of magnitude larger than our previously measured value of the π^{+}π^{-} atom ground state lifetime τ=(3.15_{-0.26}^{+0.28}|_{tot})×10^{-15}  s. Further studies of long-lived π^{+}π^{-} atoms will allow us to measure energy differences between p and s atomic states and so to discriminate between the isoscalar and isotensor ππ scattering lengths with the aim to check QCD predictions.

Cell-permeable p38 MAP kinase protects adult hippocampal neurons from cell death

p38 mitogen-activated protein (MAP) kinase (p38) is a member of the MAP kinase family. Previous reports using p38 chemical inhibitors have suggested that its activation contributes to hippocampal neuronal cell death rather than cell survival. In this study, we used both a cell-permeable p38 protein containing the HIV protein transduction domain (PTD) and cultured adult hippocampal neurons, which were differentiated from cultured adult hippocampal neural stem/progenitor cells (NPCs), to evaluate the direct function of p38 on adult hippocampal neurons. Our immunocytochemical experiments demonstrated that wild-type cell-permeable p38 protein prevents cell death of adult hippocampal neurons induced by a low glucose condition. Our findings indicate that cell-permeable p38 protein may be useful in preventing the degeneration of higher brain function occurring through hippocampal neuronal cell death, and furthermore, that the maintenance of intracellular p38 levels could be another therapeutic target for neurodegenerative diseases such as Alzheimer's disease (AD).