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Developmental Biology Jun 2017Transposable elements are parasitic genomic elements that can be deleterious for host gene function and genome integrity. Heterochromatic histone modifications are...
Transposable elements are parasitic genomic elements that can be deleterious for host gene function and genome integrity. Heterochromatic histone modifications are involved in the repression of transposons. However, it remains unknown how these histone modifications mark different types of transposons during embryonic development. Here we document the variety of heterochromatic epigenetic signatures at parasitic elements during development in Xenopus tropicalis, using genome-wide ChIP-sequencing data and ChIP-qPCR analysis. We show that specific subsets of transposons in various families and subfamilies are marked by different combinations of the heterochromatic histone modifications H4K20me3, H3K9me2/3 and H3K27me3. Many DNA transposons are marked at the blastula stage already, whereas at retrotransposons the histone modifications generally accumulate at the gastrula stage or later. Furthermore, transposons marked by H3K9me3 and H4K20me3 are more prominent in gene deserts. Using intra-subfamily divergence as a proxy for age, we show that relatively young DNA transposons are preferentially marked by early embryonic H4K20me3 and H3K27me3. In contrast, relatively young retrotransposons are marked by increasing H3K9me3 and H4K20me3 during development, and are also linked to piRNA-sized small non-coding RNAs. Our results implicate distinct repression mechanisms that operate in a transposon-selective and developmental stage-specific fashion.
Topics: Animals; Chromatin Immunoprecipitation; DNA Transposable Elements; Embryo, Nonmammalian; Embryonic Development; Epigenetic Repression; Evolution, Molecular; Gene Expression Regulation, Developmental; Heterochromatin; Histone Code; Histones; Methylation; Protein Processing, Post-Translational; RNA, Small Interfering; Retroelements; Xenopus; Xenopus Proteins
PubMed: 27639284
DOI: 10.1016/j.ydbio.2016.08.031 -
Scientific Reports Feb 2024In quantum computing, the quantum walk search algorithm is designed for locating fixed marked nodes within a graph. However, when multiple marked nodes exist, the...
In quantum computing, the quantum walk search algorithm is designed for locating fixed marked nodes within a graph. However, when multiple marked nodes exist, the conventional search algorithm lacks the capacity to simultaneously amplify the marked nodes as well as identify the correct chronological ordering between the marked nodes, if any. To address this limitation, we explore a potential extension of the algorithm by introducing additional quantum states to label the marked nodes. The labels resolve the ambiguity of simultaneous amplification of the marked nodes. Additionally, by associating the label states with a chronological ordering, we can extend the algorithm to track a moving particle on a two-dimensional surface. Our algorithm efficiently searches for the trajectory of the particle and is supported by a proposed quantum circuit. This concept holds promise for a range of applications, from real-time object tracking to network management and routing.
PubMed: 38307883
DOI: 10.1038/s41598-024-51709-0 -
Clinical and Translational... Apr 2020Hepatic encephalopathy (HE) is common in advanced cirrhosis and is characterized by marked neuropsychiatric abnormalities. However, despite its severity and effects on... (Observational Study)
Observational Study
OBJECTIVES
Hepatic encephalopathy (HE) is common in advanced cirrhosis and is characterized by marked neuropsychiatric abnormalities. However, despite its severity and effects on brain function, the impact of HE on psychological status of patients has not been adequately assessed. The aim of this study was to evaluate the effect of HE on psychological status of patients and their informal caregivers.
METHODS
Fifteen patients with cirrhosis and episodic or persistent HE and their corresponding informal caregivers were included. Semistructured interviews were performed in patients and caregivers. Quality of life (QoL) was assessed by the short-form 36 in both patients and caregivers, and the Zarit burden score was measured in caregivers. The analysis of interviews was performed using qualitative methodology.
RESULTS
HE causes a major psychological impact on patients with HE. The first episode of HE caused a very significant impact that was reported with deep feelings, mainly of fear, anger, misery, anxiety, and sorrow, which persisted with time. Symptoms causing more psychological impact on patients were impaired ability to walk and speak. All effects were associated with a marked impairment in QoL. The psychological impact was also marked in caregivers who had a major burden, as assessed by the Zarit score. Moreover, QoL, particularly the mental component score, was markedly impaired in caregivers in intensity similar to that of patients.
DISCUSSION
HE has a profound psychological impact on patients and their informal caregivers, associated with a marked negative influence on QoL. The psychological effects of HE on patients and caregivers should be evaluated and treated.
Topics: Aged; Caregivers; Cost of Illness; Female; Hepatic Encephalopathy; Humans; Liver Cirrhosis; Male; Middle Aged; Psychometrics; Qualitative Research; Quality of Life; Severity of Illness Index; Surveys and Questionnaires
PubMed: 32352686
DOI: 10.14309/ctg.0000000000000159 -
Lung Jun 2020Area under expiratory flow-volume curve (AEX) is a useful spirometric tool in stratifying respiratory impairment. The AEX approximations based on isovolumic flows can be...
BACKGROUND
Area under expiratory flow-volume curve (AEX) is a useful spirometric tool in stratifying respiratory impairment. The AEX approximations based on isovolumic flows can be used with reasonable accuracy when AEX is unavailable. We assessed here pre- to post-bronchodilator (BD) variability of AEX as a functional assessment tool for lung disorders.
METHODS
The BD response was assessed in 4330 subjects by changes in FEV, FVC, and AEX, which were derived from FVC, peak expiratory flow, and forced expiratory flow at 25%, 50%, and 75% FVC. Newly proposed BD response categories (negative, minimal, mild, moderate and marked) have been investigated in addition to standard criteria.
RESULTS
Using standard BD criteria, 24% of subjects had a positive response. Using the new BD response categories, only 23% of subjects had a negative response; 45% minimal, 18% mild, 9% moderate, and 5% had a marked BD response. Mean percent change of the square root AEX was 0.3% and 14.3% in the standard BD-negative and BD-positive response groups, respectively. In the new BD response categories of negative, minimal, mild, moderate, and marked, mean percent change of square root AEX was - 8.2%, 2.9%, 9.2%, 15.0%, and 24.8%, respectively.
CONCLUSIONS
Mean pre- to post-BD variability of AEX was < 6% and stratified well between newly proposed categories of BD response (negative, minimal, mild, moderate and marked). We suggest that AEX (AEX) could become a useful measurement for stratifying dysfunction in obstructive lung disease and invite further investigation into indications for using bronchodilator agents or disease-modifying, anti-inflammatory therapies.
Topics: Aged; Bronchodilator Agents; Exhalation; Female; Forced Expiratory Volume; Humans; Male; Middle Aged; Pulmonary Disease, Chronic Obstructive; Retrospective Studies; Spirometry; Vital Capacity
PubMed: 32211978
DOI: 10.1007/s00408-020-00345-2 -
Breast Cancer (Tokyo, Japan) Jul 2022To compare the diagnostic performances of contrast-enhanced digital mammography (CEDM) and breast MRI in evaluations of breast cancer, with a focus on the impact of...
Impact of background parenchymal enhancement levels on the diagnosis of contrast-enhanced digital mammography in evaluations of breast cancer: comparison with contrast-enhanced breast MRI.
PURPOSE
To compare the diagnostic performances of contrast-enhanced digital mammography (CEDM) and breast MRI in evaluations of breast cancer, with a focus on the impact of background parenchymal enhancement (BPE) levels.
METHODS
The present study included women who underwent CEDM and breast MRI to evaluate the disease extent of breast cancer between January 2018 and December 2019. Readers judged BPE levels (minimal-mild or moderate-marked) on CEDM, and were asked to assign findings suggesting malignancy using the following criteria: (1) enhancement other than BPE and (2) BI-RADS 4/5 calcifications without enhancement. On MRI, BI-RADS 3 and BI-RADS 4/5 lesions were evaluated as benign and malignant, respectively. The diagnostic performances of CEDM and MRI were compared separately between women with minimal-mild BPE and those with moderate-marked BPE.
RESULTS
Sixty-nine patients comprising 43 postmenopausal and 26 premenopausal women were included in the present study. In total, 195 lesions (94 malignant and 101 benign) were identified. The sensitivity and specificity of CEDM for the diagnosis of all lesions were 90.8 and 91.5% with minimal-mild BPE and 79.3 and 76.2% with moderate-marked BPE, respectively. The sensitivity and specificity of MRI were 90.0% and 71.0% with minimal-mild BPE and 87.5% and 78.1% with moderate-marked BPE, respectively. The accuracy of CEDM was significantly superior to that of MRI in women with minimal-mild BPE on both CEDM and MRI (p = 0.002). Regarding the negative impact of a correct diagnosis on CEDM, the odds ratio of "moderate-marked BPE" was 0.382.
CONCLUSION
In patients with minimal-mild BPE, the diagnostic performance of CEDM was superior to that of MRI.
Topics: Breast; Breast Neoplasms; Contrast Media; Female; Humans; Magnetic Resonance Imaging; Mammography; Retrospective Studies
PubMed: 35220511
DOI: 10.1007/s12282-022-01345-1 -
Korean Journal of Radiology 2018To determine the histopathologic features associated with ultrasonographic echogenicity of thyroid nodules.
OBJECTIVE
To determine the histopathologic features associated with ultrasonographic echogenicity of thyroid nodules.
MATERIALS AND METHODS
This study included 95 nodules of 95 patients (76 women, 19 men; mean age 47.5 ± 12.9 years) with homogeneous echogenicity in which core needle biopsy was performed during a one year period. The nodule echogenicity was categorized into 4 grades (hyperechogenicity, isoechogenicity, mild hypoechogenicity, and marked hypoechogenicity). The biopsy specimens were evaluated by a pathologist regarding the histopathologic features of fibrosis, lymphoid infiltration, microfollicular pattern, uniform follicular pattern, and hypercellularity in nodules. We evaluated the association of each histopathologic feature among 3 categories of nodule echogenicity by multinomial regression analysis.
RESULTS
The nodule echogenicity was isoechoic in 28 (29.5%), mildly hypoechoic in 37 (38.9%), and markedly hypoechoic in 30 (31.6%), and there was no hyperechoic nodule. There was a trend of increasing frequency of fibrosis (> 30%) as nodule echogenicity decreased (isoechogenicity, 10.7%; mild hypoechogenicity, 32.4%; and marked hypoechogenicity, 80%; < 0.001). The microfollicular pattern, uniform follicular pattern, and hypercellularity were frequently found in mildly hypoechoic nodules than in isoechoic nodules ( ≤ 0.018). The fibrosis (> 30%) and hypercellularity were independently associated with mild or marked hypoechogenicity as compared to isoechogenicity (fibrosis; ≤ 0.004 and hypercellularity; ≤ 0.036), and only fibrosis (> 30%) was independently associated with marked hypoechogenicity as compared to mild hypoechogenicity ( = 0.004).
CONCLUSION
The fibrosis (> 30%) and high cellularity are independently associated with mild or marked hypoechogenicity of nodules. The knowledge of the relationship of echogenicity and histopathology of thyroid nodules could improve management of patients with thyroid nodules.
Topics: Adult; Biopsy, Fine-Needle; Biopsy, Large-Core Needle; Female; Fibrosis; Humans; Logistic Models; Male; Middle Aged; Retrospective Studies; Thyroid Nodule; Ultrasonography
PubMed: 29962873
DOI: 10.3348/kjr.2018.19.4.673 -
Hormones (Athens, Greece) Mar 2023Metanephrines (MTNs) are metabolites of catecholamines and are constantly produced in high amounts by pheochromocytomas and paragangliomas (PPGLs). Marked MTN elevations...
INTRODUCTION
Metanephrines (MTNs) are metabolites of catecholamines and are constantly produced in high amounts by pheochromocytomas and paragangliomas (PPGLs). Marked MTN elevations (> 3 times the upper limit of normal [ULN]) are highly suggestive of PPGL. The frequency of marked MTN elevations in non-PPGL hypertensive emergencies (HTNEs) is unknown.
METHODS
We retrospectively analyzed plasma free metanephrine (PMTN) and 24-h urinary fractionated metanephrine (UMTN) levels in 48 consecutive patients (59.7 ± 15.6 years; 48% female; BMI: 31 ± 9.7 kg/m) hospitalized for HTNE, defined as systolic blood pressure (SBP) > 180 mmHg or diastolic blood pressure (DBP) > 120 mmHg with end-organ damage. PMTNs were measured in 47 patients, UMTNs were measured in 16 patients, and both PMTNs and UMTNs were measured in 15 patients.
RESULTS
PMTN/UMTN levels were not associated with SBP/DBP, comorbidities, end-organ damage, or interfering medications, the exception being that plasma normetanephrines (PNMNs) were significantly associated with comorbidities (Adj. R = 0.16; p = 0.04) and interfering medications (Adj. R = 0.15; p = 0.03), although with weak correlation. Marked MTN (specifically PNMN) elevations (647, 521, and 453 pg/mL; normal ≤ 148 pg/mL) were noted in only three patients (6%).
DISCUSSION
Marked MTN elevations in HTNE are uncommon. Therefore, we recommend against measuring MTN in the setting of an apparent precipitating cause of HTNE to avoid unnecessary testing and imaging. Testing for MTN in HTNE should be pursued only when there is no clear precipitating cause and in cases where there is strong underlying clinical suspicion for PPGL. However, should testing be performed, marked MTN elevations should not be disregarded as being a commonly occurring result of HTNE.
Topics: Humans; Female; Male; Metanephrine; Retrospective Studies; Pheochromocytoma; Paraganglioma; Adrenal Gland Neoplasms
PubMed: 36596928
DOI: 10.1007/s42000-022-00422-6 -
Histopathology Aug 2016To elucidate the histopathological findings of classical Lambl excrescences (LEs) and non-exophytic LEs (non-ex LEs) without excrescent papillary features.
AIMS
To elucidate the histopathological findings of classical Lambl excrescences (LEs) and non-exophytic LEs (non-ex LEs) without excrescent papillary features.
METHODS AND RESULTS
We examined 126 aortic valves (AVs) and revealed LEs (non-ex and/or classical), non-ex LEs and classical LEs in 106, 78 and 88 AVs, respectively. The detection of non-ex LEs was challenging, but elastica van Gieson stain highlighted their presence. Non-ex and classical LEs chiefly involved the ventricular regions, favoured posterior cusps and coexisted in the same areas of 31 AVs. A possible transformation of classical LEs into non-ex LEs was suggested histologically in 39 AVs. Non-ex LEs were associated with age of >70 years (P < 0.001) and marked deformity (P = 0.007). Classical LEs were associated inversely with marked deformity (P < 0.001), but not with age of >70 years. Compared with age- and sex-matched control AVs, non-ex LEs and marked deformity in dysfunctional AVs were more common (P = 0.037 and P < 0.001, respectively), but classical LEs were less common (P = 0.021).
CONCLUSIONS
Non-ex LEs have subtle features but are a common form of LEs, and seem to develop from classical LEs. AV dysfunction-related marked deformity can promote non-ex LEs.
Topics: Adult; Aged; Aged, 80 and over; Aortic Valve; Female; Heart Valve Diseases; Humans; Male; Middle Aged
PubMed: 26825675
DOI: 10.1111/his.12938 -
Natural Language & Linguistic Theory 2023Based on six detailed case studies of languages in which focus is marked morphosyntactically, we propose a novel formal theory of focus marking, which can capture these...
Based on six detailed case studies of languages in which focus is marked morphosyntactically, we propose a novel formal theory of focus marking, which can capture these as well as the familiar English-type prosodic focus marking. Special attention is paid to the patterns of focus syncretism, that is, when different size and/or location of focus are indistinguishably realized by the same form. The key ingredients to our approach are that complex constituents (not just words) may be directly focally marked, and that the choice of focal marking is governed by blocking.
PubMed: 37969619
DOI: 10.1007/s11049-023-09567-4 -
Animal Cognition Nov 2021Responses to mirrors vary in non-human animals. Many species respond socially to mirrors with relatively few species demonstrating self-recognition in mirrors. In this...
Responses to mirrors vary in non-human animals. Many species respond socially to mirrors with relatively few species demonstrating self-recognition in mirrors. In this study, we investigated the responses of ferrets to mirrors. Six adult ferrets (3 males, 3 females, all over a year old) were exposed to mirrors and their responses were investigated over three experimental conditions (baseline, mirror preference, mark test) in a repeated measures design. Upon initial presentation, the ferrets showed more approach and sniffing behaviour toward the mirror than the non-reflective surface. The ferrets also showed a preference for the mirror and spent more time in close proximity to the mirror than the non-reflective surface. In the mirror mark test, the ferrets showed more approach, sniffing and self-exploration behaviour when they were marked and presented with the mirror compared to when they were marked and presented with the non-reflective surface, or when they were sham-marked and presented with either surface. Our findings are suggestive that ferrets show interest in mirrors and that further study exploring the responses of ferrets to mirrors is warranted.
Topics: Animals; Behavior, Animal; Female; Ferrets; Male
PubMed: 34086108
DOI: 10.1007/s10071-021-01523-2