bluuebunny/crossref_metadata_2025 huggingface dataset:
New assessment of the fast ion energy in ASDEX upgrade H-mode discharges
Authors: Tardini G. , Weiland M. , Angioni C. , Cavedon M. , Ryter F. , Schneider P.A. , Upgrade Team The ASDEX
Published: December 2020

Confinement scaling laws such as IPB98(y, 2) are widely used to extrapolate the performance of present tokamaks to next-step devices such as ITER or DEMO. The thermal energy of the plasma (W
th), which is used to determine the energy confinement time for most scaling laws, is difficult to measure, due to the sizeable uncertainties in the experimental kinetic profiles. The common approach in the tokamak community is to derive W
th as the difference between the measured magnetohydrodynamic (MHD) energy and some simulation-based estimate of the fast ion energy W
fi. In H-mode plasmas W
fi can be as high as W
th, in presence of neutral beam injection (NBI) or ion cyclotron radio frequency heating (ICRF), therefore an accurate assessment of W
fi is crucial to have a somewhat reliable H-factor, regardless of the power-scaling of a given scaling law. In this paper we aim at evaluating the current approach to estimate W
fi, by comparing its predictions with a wide database of calculations using validated NBI codes. Systematic deviations and trends, as well as statistical scatter are discussed. We use a comprehensive database of AUG H-mode deuterium plasmas, with significant variations of plasma current, NBI power and plasma density. We neglect thereby the fast-ion losses caused by MHD modes and the synergy effect between NBI and ICRF. A new approach is proposed based on the newly developed fast NBI code RABBIT.
Robust domain variants and ferroelectric property in epitaxial BiFeO3 films
Authors: Qiao Xiaojun , Geng Wenping , Meng Jianwei , Sun Yao , Bi Kaixi , Yang Yun , Yu Junbin , He Jian , Chou Xiujian
Published: December 2020

Lead-free ferroelectric thin films have great potential for electric devices owing to the dramatically expanding information epoch. Exploring the domain engineering and temperature stability of ferroelectric films are still urgent since these polarization dipoles are sensitive to external effects. In this work, the temperature dependence of domain dynamic and local piezoelectric response were investigated in epitaxial BiFeO3 (BFO) thin films prepared by pulse leaser deposition (PLD) technology, which exhibiting well-defined polarization switchable intrinsic property. Regarding to temperature endurance, domain variants remain quite stable state regarding to both the vertical and lateral direction, which is in consistent with the free-energy minimum competition theory. Besides, the piezoelectric response along vertical and lateral direction exhibit good temperature endurance. This work demonstrates thin films with rather stable ferroelectric states, which show not only exploration on domain dynamic corresponding to temperature influence, but also promising potential application in electrical storage devices especially working under high temperature.
Study on UV-aging performance of fluorinated polymer coating and application on painted muds
Authors: Huang Hongpu , Guo Hong , Feng Yefeng
Published: December 2020

The UV-aging tests were carried out on synthetic fluorinated polymer coating (poly (methyl methacrylate)-poly (dodecafluoroheptyl methacrylate), FP) to study its UV-aging mechanism, UV-aging resistance and application on painted muds with calcium carbonate, azurite, haematitum, mineral green and cinnabar pigments. The UV-aging mechanism was studied by Fourier infrared spectroscopy attenuated total reflection technique (ATR-FTIR) and x-ray photoelectron spectroscopy (XPS). The UV-aging resistance of FP was characterized by field emission scanning electron microscope (SEM), CR-400 color difference meter and static contact angle (SCA). The FP was applied on the painted muds samples and the protective efficacy was evaluated by measuring the chromatic variations(ΔE) and water contact angles of samples after treatment. The results of ATR-FTIR and XPS shown that FP only had microphase separation without chemical change after 360h of aging. After 360h of aging, the SEM shown that there were just some bumps on the FP film surface and further proved the phenomenon of microphase separation; the color change of the FP film was no difference (ΔE = 0.46); the FP film could retain adequate hydrophobicity (101.0°). After the painted muds samples were treated by FP, the color change of the calcium carbonate and haematitum was just noticeable difference (ΔE = 0.80 ∼ 1.49), while the color change of the azurite, mineral green and cinnabar was fairly large difference (ΔE = 4.4 ∼ 6.3); all pigments could maintain hydrophobicity at the end of aging. All the results demonstrated that the FP has excellent UV-aging resistance and could provide adequate protective efficacy for calcium carbonate and haematitum, but the protection efficacy for the azurite, mineral green and cinnabar is not ideal. Thus, it is believed that the FP can be used as a suitable UV resistant protective coating for calcium carbonate and haematitum.
Quantum versus classical generative modelling in finance
Authors: Coyle Brian , Henderson Maxwell , Chan Jin Le Justin , Kumar Niraj , Paini Marco , Kashefi Elham
Published: December 2020

Finding a concrete use case for quantum computers in the near term is still an open question, with machine learning typically touted as one of the first fields which will be impacted by quantum technologies. In this work, we investigate and compare the capabilities of quantum versus classical models for the task of generative modelling in machine learning. We use a real world financial dataset consisting of correlated currency pairs and compare two models in their ability to learn the resulting distribution—a restricted Boltzmann machine, and a quantum circuit Born machine. We provide extensive numerical results indicating that the simulated Born machine always at least matches the performance of the Boltzmann machine in this task, and demonstrates superior performance as the model scales. We perform experiments on both simulated and physical quantum chips using the Rigetti QCSTM platform, and also are able to partially train the largest instance to date of a quantum circuit Born machine on quantum hardware. Finally, by studying the entanglement capacity of the training Born machines, we find that entanglement typically plays a role in the problem instances which demonstrate an advantage over the Boltzmann machine.
Theoretical investigation of the negative ionization of hydrogen particles on metal surfaces with low work function
Authors: Gainullin I K , Dudnikov V G
Published: December 2020

This work addresses the negative ionization of hydrogen particles on low work function metal surfaces, which is an important process for the field of the surface plasma negative ion beams sources. We present the theoretical model for the computer calculation of the negative ionization probability which takes into account the component of atom/ion velocity, parallel to the surface. The calculated negative ionization probability of hydrogen quantitatively fits to the experimental data in the wide range of ion exit energies. The theoretical estimation shows, that for the low work function converter surfaces (φ ∼ 1.5 eV) the negative ionization probability of hydrogen can be enhanced up to 30% if the hydrogen has velocity component parallel to the surface ∼0.05 a.u. (∼60 eV). Therefore, the H- ion production rate can be increased for a negative ion source configuration that implements the oblique exit angle of hydrogen.
Litigating socio-economic and women’s rights in Benin’s constitutional court
Authors: Kang Alice J , Wing Susanna D
Published: December 2020

Scholars debate the role of legal institutions in promoting human rights in Africa. Much of the discussion focuses on Anglophone countries and does not examine the gender of litigants. We propose a constitutionalism constrained perspective that argues that which and whose rights are adjudicated are shaped by the context of constitutional reform. Where reformists are primarily concerned with safeguarding civil and political rights, high courts may protect civil and political rights claims more often than socio-economic ones. Examining hundreds of human rights decisions issued by Benin’s Constitutional Court, we ask, which and whose rights does the court protect? We find the court is more likely to reject litigants’ claims on technical grounds when the issues involve socio-economic rights than when they concern civil or political rights. When a case is heard, moreover, the court finds violations of civil and political rights more often than socio-economic rights. Further, we find that an overwhelming percentage of litigants are men; women rarely appear as petitioners, although when women’s claims are heard, they are just as likely to succeed. Our findings about socio-economic rights and gender in Benin’s Constitutional Court have broader implications for understanding the limitations of constitutional reform.
The value of ambulatory blood pressure measurement to detect masked diastolic hypotension in older patients treated for hypertension
Authors: Kleipool Emma E F , Rozendaal Eva S , Mahadew Shaya K N , Kramer Mark H H , van den Born Bert-Jan H , Serné Erik H , Peters Mike J L , Muller Majon
Published: December 2020

Objective

assess how many patients with low ambulatory diastolic blood pressure (DBP) are not identified when relying on office DBP alone, and thus have ‘masked diastolic hypotension’.

Design

cross-sectional, retrospective cohort study.

Setting

academic hospital.

Subjects

848 patients treated for hypertension who received ambulatory blood pressure monitoring (ABPM).

Methods

cut-off value between on- and off-target systolic blood pressure (SBP): 140 mmHg. Cut-off for low office and/or ambulatory DBP: DBP ≤ 70 mmHg. ‘Masked diastolic hypotension’ was defined as office DBP > 70 mmHg and mean ambulatory DBP ≤ 70 mmHg.

Results

mean age of the sample was 60 ± 13 years, 50% was female, 37% had diabetes, 42% preexisting cardiovascular disease (CVD), mean office blood pressure (BP) was 134/79 mmHg. In all patients (n = 848), low office DBP was present in n = 84(10%), while n = 183(22%) had low ambulatory DBP. In all patients with normal-to-high office DBP (n = 764), n = 122(16%) had ‘masked diastolic hypotension’. In this group, ambulatory DBP was 14–19 mmHg lower than office DBP. Patients with low ambulatory DBP were older, had more (cardiovascular) comorbidities, and used more (antihypertensive) drugs. Antihypertensive drugs were lowered or discontinued in 30% of all patients with ‘masked diastolic hypotension’ due to side effects.

Conclusions

‘masked diastolic hypotension’ is common among patients treated for hypertension, particularly in older patients with CVD (e.g. coronary artery disease, diabetes), patient groups in which the European Society of Cardiology/Hypertension guideline advises to prevent low DBP. Although it remains to be examined at which BP levels the harms of low DBP outweigh the benefits of lowering SBP, our observations are aimed to increase awareness among physicians.
Rapid review of decision-making for place of care and death in older people: lessons for COVID-19
Authors: West Emily , Moore Kirsten , Kupeli Nuriye , Sampson Elizabeth L , Nair Pushpa , Aker Narin , Davies Nathan
Published: December 2020

Introduction

The coronavirus pandemic (COVID-19) has affected the functioning and capacity of healthcare systems worldwide. COVID-19 has also disproportionately affected older adults. In the context of COVID-19, decision-making surrounding place of care (PoC) and place of death (PoD) in older adults involves significant new challenges.

Aims

To explore key factors that influence PoC and PoD decisions in older adults. A secondary aim was to investigate key factors that influence the process and outcome of these decisions in older adults. To apply findings from current evidence to the context of COVID-19.

Methods

Rapid review of reviews, undertaken using WHO guidance for rapid reviews for the production of actionable evidence. Data extracted was synthesised using narrative synthesis, with thematic analysis and tabulation.

Results

10 papers were included for full data extraction. These papers were published between 2005 and 2020. Papers included discussed actual PoD, as well as preferred. Results were divided into papers that explored the process of decision-making, and those that explored decision-making outcomes.

Conclusions

The process and outcomes of decision-making for older people are affected by many factors—all of which have the potential to influence both patients and caregivers experience of illness and dying. Within the context of COVID-19, such decisions may have to be made rapidly and be reflexive to changing needs of systems and of families and patients.
GuidePro: a multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts
Authors: He Wei , Wang Helen , Wei Yanjun , Jiang Zhiyun , Tang Yitao , Chen Yiwen , Xu Han
Published: December 2020

Motivation

The efficiency of CRISPR/Cas9-mediated protein knockout is determined by three factors: sequence-specific sgRNA activity, frameshift probability and the characteristics of targeted amino acids. A number of computational methods have been developed for predicting sgRNA efficiency from different perspectives. However, an integrative method that combines all three factors for rational sgRNA selection is still lacking.

Results

We developed GuidePro, a two-layer ensemble predictor that enables the integration of multiple factors for the prioritization of sgRNAs in protein knockouts. Tested on independent datasets, GuidePro outperforms existing methods and demonstrates consistent superior performance in predicting phenotypes caused by protein loss-of-function, suggesting its robustness for prioritizing sgRNAs in various applications of CRISPR/Cas9 knockouts.

Availability and implementation

GuidePro is available at https://github.com/MDhewei/GuidePro. A web application for prioritizing sgRNAs that target protein-coding genes in human, monkey and mouse genomes is available at https://bioinformatics.mdanderson.org/apps/GuidePro.

Supplementary information

Supplementary data are available at Bioinformatics online.
Brainstem and striatal volume changes are detectable in under 1 year and predict motor decline in spinocerebellar ataxia type 1
Authors: Koscik Timothy R , Sloat Lauren , van der Plas Ellen , Joers James M , Deelchand Dinesh K , Lenglet Christophe , Öz Gülin , Nopoulos Peggy C
Published: December 2020

Spinocerebellar ataxia type 1 is a progressive neurodegenerative, movement disorder. With potential therapies on the horizon, it is critical to identify biomarkers that (i) differentiate between unaffected and spinocerebellar ataxia Type 1-affected individuals; (ii) track disease progression; and (iii) are directly related to clinical changes of the patient. Magnetic resonance imaging of volumetric changes in the brain may be a suitable source of biomarkers for spinocerebellar ataxia Type 1. In a previous report on a longitudinal study of patients with spinocerebellar ataxia Type 1, we evaluated the volume and magnetic resonance spectroscopy measures of the cerebellum and pons, showing pontine volume and pontine N-acetylaspartate-to-myo-inositol ratio were sensitive to change over time. As a follow-up, the current study conducts a whole brain exploration of volumetric MRI measures with the aim to identify biomarkers for spinocerebellar ataxia Type 1 progression. We adapted a joint label fusion approach using multiple, automatically generated, morphologically matched atlases to label brain regions including cerebellar sub-regions. We adjusted regional volumes by total intracranial volume allowing for linear and power-law relationships. We then utilized Bonferroni corrected linear mixed effects models to (i) determine group differences in regional brain volume and (ii) identify change within affected patients only. We then evaluated the rate of change within each brain region to identify areas that changed most rapidly. Lastly, we used a penalized, linear mixed effects model to determine the strongest brain predictors of motor outcomes. Decrease in pontine volume and accelerating decrease in putamen volume: (i) reliably differentiated spinocerebellar ataxia Type 1-affected and -unaffected individuals; (ii) were observable in affected individuals without referencing an unaffected comparison group; (iii) were detectable within ∼6–9 months; and (iv) were associated with increased disease burden. In conclusion, volumetric change in the pons and putamen may provide powerful biomarkers to track disease progression in spinocerebellar ataxia Type 1. The methods employed here are readily translatable to current clinical settings, providing a framework for study and usage of volumetric neuroimaging biomarkers for clinical trials.
Infant Exposure to Dolutegravir Through Placental and Breast Milk Transfer: A Population Pharmacokinetic Analysis of DolPHIN-1
Authors: Dickinson Laura , Walimbwa Stephen , Singh Yashna , Kaboggoza Julian , Kintu Kenneth , Sihlangu Mary , Coombs Julie-Anne , Malaba Thokozile R , Byamugisha Josaphat , Pertinez Henry , Amara Alieu , Gini Joshua , Else Laura , Heiberg Christie , Hodel Eva Maria , Reynolds Helen , Myer Landon , Waitt Catriona , Khoo Saye , Lamorde Mohammed , Orrell Catherine ,   DolPHIN-1 Study Group, Nakijoba Ritah , Kyohairwe Isabella , Magoola Johnson , Ssempija Emmanuel
Published: December 2020

Background

Rapid reduction in human immunodeficiency virus (HIV) load is paramount to prevent peripartum transmission in women diagnosed late in pregnancy. We investigated dolutegravir population pharmacokinetics in maternal plasma, umbilical cord, breast milk, and infant plasma samples from DolPHIN-1 participants (NCT02245022) presenting with untreated HIV late in pregnancy (28–36 weeks gestation).

Methods

Pregnant women from Uganda and South Africa were randomized (1:1) to daily dolutegravir (50 mg/d) or efavirenz-based therapy. Dolutegravir pharmacokinetic sampling (0–24 hours) was undertaken 14 days after treatment initiation and within 1–3 weeks after delivery, with matched maternal and cord samples at delivery. Mothers were switched to efavirenz, and maternal and infant plasma and breast milk samples were obtained 24, 48, or 72 hours after the switch. Nonlinear mixed-effects modeling was used to describe dolutegravir in all matrices and to evaluate covariates.

Results

A total of 28 women and 22 infants were included. Maternal dolutegravir was described by a 2-compartment model linked to a fetal and breast milk compartment. Cord and breast milk to maternal plasma ratios were 1.279 (1.209–1.281) and 0.033 (0.021–0.050), respectively. Infant dolutegravir was described by breast milk–to–infant and infant elimination rate constants. No covariate effects were observed. The median predicted infant dolutegravir half-life and median time to protein-adjusted 90% inhibitory concentration (0.064 mg/L) for those above this threshold were 37.9 (range, 22.1–63.5) hours and 108.9 (18.6–129.6) hours (4.5 [0.8–5.4] days) (n = 13), respectively.

Conclusions

Breastfeeding contributed relatively little to infant plasma exposure, but a median of 4.5 days of additional prophylaxis to some of the breastfed infants was observed after cessation of maternal dolutegravir (3–15 days postpartum), which waned with time postpartum as transplacental dolutegravir cleared.
Approaches to treat pulmonary arterial hypertension by targeting BMPR2: from cell membrane to nucleus
Authors: Dunmore Benjamin J , Jones Rowena J , Toshner Mark R , Upton Paul D , Morrell Nicholas W
Published: December 2020

Pulmonary arterial hypertension (PAH) is estimated to affect between 10 and 50 people per million worldwide. The lack of cure and devastating nature of the disease means that treatment is crucial to arrest rapid clinical worsening. Current therapies are limited by their focus on inhibiting residual vasoconstriction rather than targeting key regulators of the cellular pathology. Potential disease-modifying therapies may come from research directed towards causal pathways involved in the cellular and molecular mechanisms of disease. It is widely acknowledged that targeting reduced expression of the critical bone morphogenetic protein type-2 receptor and its associated signalling pathways is a compelling therapeutic avenue to explore. In this review, we highlight the advances that have been made in understanding this pathway and the therapeutics that are being tested in clinical trials and the clinic to treat PAH.
Exercise cardiac magnetic resonance imaging to assess dynamic right ventricular outflow tract obstruction in congenital heart disease: a case report
Authors: Santens Béatrice , De Bosscher Ruben , Budts Werner , Bogaert Jan
Published: December 2020

Background

Right ventricular outflow tract obstruction in patients with congenital heart disease is usually assessed using echocardiographic peak instantaneous gradient at rest. Since right ventricular outflow tract obstruction may change during exercise (dynamic right ventricular outflow tract obstruction), we present a case emphasizing the potential use of exercise cardiac magnetic resonance imaging (CMR).

Case summary

We discuss a 15-year-old patient with repaired mid-ventricular sub-pulmonary stenosis type double-chambered right ventricle causing right ventricular outflow tract obstruction and symptoms on exertion. In this case, exercise CMR imaging provided additional information, allowing adequate surgical planning.

Discussion

The additional value of exercise CMR imaging in a case of right ventricular outflow tract obstruction was described. Although exercise cardiac magnetic resonance imaging did not show a significant increase in peak gradient across the right ventricular outflow tract obstruction, shifting and D-shaping of the interventricular septum with subsequent insufficient left ventricular filling (preload) was observed in the patient with recurrent double-chambered right ventricle. This case demonstrates how exercise CMR imaging can be helpful in the clinical decision beyond standard echocardiographic evaluation by providing additional evidence of adverse haemodynamics during exercise.
Primary sutureless repair for infracardiac total anomalous pulmonary venous connection
Authors: Liufu Rong , Liu Xiaobing , Liu Tao , Chen Jimei , Wen Shusheng , Cen Jianzheng , Zhuang Jian
Published: December 2020

OBJECTIVES

This study aimed to review surgical experiences in patients with infracardiac total anomalous pulmonary venous connection (TAPVC).

METHODS

This retrospective study included 63 infants who underwent conventional repair (n = 27) and sutureless repair (n = 36) from 1 February 2009 to 31 June 2019. Kaplan–Meier curves and Cox regressions were applied to analyse the overall survival and risk factors. Cumulative incidence curves and competing risk models were used to evaluate postoperative pulmonary venous obstruction (PVO).

RESULTS

There were 4 hospital deaths and 2 late deaths, and 8 patients experienced postoperative PVO. The survival rates at 30 days, 1 year and 5 years were 95.2%, 90.5% and 90.5%, respectively. The overall survival rate was significantly higher in the sutureless group than that in the conventional group. The cumulative incidence of postoperative PVO in the conventional group was higher than that in the sutureless group. Univariable Cox regression analyses showed that lower surgical weight, increase in preoperative international normalized ratio, prolonged cardiopulmonary bypass time and aortic cross-clamp time and longer duration of postoperative ventilation were associated with higher mortality. Longer cardiopulmonary bypass time, lower preoperative prothrombin activity and the increasing preoperative international normalized ratio before surgical repair were associated with a higher incidence of postoperative PVO.

CONCLUSIONS

Both sutureless and conventional repairs for patients with infracardiac TAPVC achieved favourable postoperative outcomes. There was no death in the sutureless repair group. Compared to conventional repair, sutureless repair was associated with lower mortality and lower incidence of restenosis in pulmonary veins and anastomosis.
Postoperative spinal cord ischaemia: magnetic resonance imaging and clinical features
Authors: Yasuda Naomi , Kuroda Yosuke , Ito Toshiro , Sasaki Masanori , Oka Shinichi , Ukai Ryo , Nakanishi Keitaro , Mikami Takuma , Shibata Tsuyoshi , Harada Ryo , Naraoka Shuichi , Kamada Takeshi , Kawaharada Nobuyoshi
Published: December 2020

OBJECTIVES

Ischaemic spinal cord injury (SCI) is one of the most serious complications of aortic surgery. Ischaemic SCIs occur due to various aetiologies, and prediction of the risk is difficult. Magnetic resonance imaging (MRI) is useful to detect the details of spinal cord infarction. There are few studies about MRI for evaluating ischaemic SCI after cardiovascular surgery and aortic events. We report 9 cases of postoperative ischaemic SCI and analyse their MRI features.

METHODS

T2-weighted MRI scans of 9 patients who developed ischaemic SCI due to cardiovascular surgery and aortic events between 2012 and 2017 were evaluated.

RESULTS

In all patients, high-intensity areas were observed on T2-weighted magnetic resonance images. The site of infarction was the thoracic spinal cord level (9 cases) and additionally at the lumbar spinal cord level (5 cases). The area of infarction area was categorized based on the arterial territory: anterior spinal artery territory (3 cases), posterior spinal artery territory (2 cases), spinal sulcal artery territory (1 case) and artery of Adamkiewicz territory (3 cases).

CONCLUSIONS

MRI revealed the infarction sites in all cases and the differences in the infarction patterns in each case. MRI could thus be useful for investigating the aetiology of ischaemic SCI following aortic surgeries and events.
Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments
Authors: Zeng Xiang , Zhang Yaolei , Meng Lingfeng , Fan Guangyi , Bai Jie , Chen Jianwei , Song Yue , Seim Inge , Wang Congyan , Shao Zenghua , Liu Nanxi , Lu Haorong , Fu Xiaoteng , Wang Liping , Liu Xin , Liu Shanshan , Shao Zongze
Published: December 2020

Background

The scaly-foot snail (Chrysomallon squamiferum) is highly adapted to deep-sea hydrothermal vents and has drawn much interest since its discovery. However, the limited information on its genome has impeded further related research and understanding of its adaptation to deep-sea hydrothermal vents.

Findings

Here, we report the whole-genome sequencing and assembly of the scaly-foot snail and another snail (Gigantopelta aegis), which inhabits similar environments. Using Oxford Nanopore Technology, 10X Genomics, and Hi-C technologies, we obtained a chromosome-level genome of C. squamiferum with an N50 size of 20.71 Mb. By constructing a phylogenetic tree, we found that these 2 deep-sea snails evolved independently of other snails. Their divergence from each other occurred ∼66.3 million years ago. Comparative genomic analysis showed that different snails have diverse genome sizes and repeat contents. Deep-sea snails have more DNA transposons and long terminal repeats but fewer long interspersed nuclear elements than other snails. Gene family analysis revealed that deep-sea snails experienced stronger selective pressures than freshwater snails, and gene families related to the nervous system, immune system, metabolism, DNA stability, antioxidation, and biomineralization were significantly expanded in scaly-foot snails. We also found 251 H-2 Class II histocompatibility antigen, A-U α chain-like (H2-Aal) genes, which exist uniquely in the Gigantopelta aegis genome. This finding is important for investigating the evolution of major histocompatibility complex (MHC) genes.

Conclusion

Our study provides new insights into deep-sea snail genomes and valuable resources for further studies.
High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis
Authors: Gao Qionghua , Xiong Zijun , Larsen Rasmus Stenbak , Zhou Long , Zhao Jie , Ding Guo , Zhao Ruoping , Liu Chengyuan , Ran Hao , Zhang Guojie
Published: December 2020

Background

Ants with complex societies have fascinated scientists for centuries. Comparative genomic and transcriptomic analyses across ant species and castes have revealed important insights into the molecular mechanisms underlying ant caste differentiation. However, most current ant genomes and transcriptomes are highly fragmented and incomplete, which hinders our understanding of the molecular basis for complex ant societies.

Findings

By hybridizing Illumina, Pacific Biosciences, and Hi-C sequencing technologies, we de novo assembled a chromosome-level genome for Monomorium pharaonis, with a scaffold N50 of 27.2 Mb. Our new assembly provides better resolution for the discovery of genome rearrangement events at the chromosome level. Analysis of full-length isoform sequencing (ISO-seq) suggested that ∼15 Gb of ISO-seq data were sufficient to cover most expressed genes, but the number of transcript isoforms steadily increased with sequencing data coverage. Our high-depth ISO-seq data greatly improved the quality of gene annotation and enabled the accurate detection of alternative splicing isoforms in different castes of M. pharaonis. Comparative transcriptome analysis across castes based on the ISO-seq data revealed an unprecedented number of transcript isoforms, including many caste-specific isoforms. We also identified a number of conserved long non-coding RNAs that evolved specifically in ant lineages and several that were conserved across insect lineages.

Conclusions

We produced a high-quality chromosome-level genome for M. pharaonis, which significantly improved previous short-read assemblies. Together with full-length transcriptomes for all castes, we generated a highly accurate annotation for this ant species. These long-read sequencing results provide a useful resource for future functional studies on the genetic mechanisms underlying the evolution of social behaviors and organization in ants.
Making experimental data tables in the life sciences more FAIR: a pragmatic approach
Authors: Jacob Daniel , David Romain , Aubin Sophie , Gibon Yves
Published: December 2020

Making data compliant with the FAIR Data principles (Findable, Accessible, Interoperable, Reusable) is still a challenge for many researchers, who are not sure which criteria should be met first and how. Illustrated with experimental data tables associated with a Design of Experiments, we propose an approach that can serve as a model for research data management that allows researchers to disseminate their data by satisfying the main FAIR criteria without insurmountable efforts. More importantly, this approach aims to facilitate the FAIR compliance process by providing researchers with tools to improve their data management practices.
Predictive risk factors for intra-abdominal hypertension after cardiac surgery
Authors: Tyson Nathan , Efthymiou Christopher
Published: December 2020

A best evidence topic in cardiac surgery was written according to a structured protocol. The question addressed was is it possible to identify predictive risk factors for the development of intra-abdominal hypertension (IAH) or abdominal compartment syndrome after cardiac surgery. Altogether 131 papers were found using the reported search, of which 7 represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. A total of 755 patients were included, with the incidence of IAH between 26.9% and 83.3%. The limited evidence on IAH after cardiac surgery should be interpreted with caution. Obesity is a strong predictor of postoperative IAH, although not confined to a central pattern and body mass index is correlated with intra-abdominal pressure (IAP). Prolonged cardiopulmonary bypass and aortic cross-clamp time predisposed to IAH in 4 cohorts. IAH in cardiac surgery patients is associated with hepatic and renal impairment, and corresponding biochemical markers may be helpful in screening, although lacking specificity. In contrast to the development of IAH in other settings, the evidence for the role of fluid balance is poor. Accurate prediction of IAH remains elusive. Based on the available evidence, routine IAP measurement should be considered postoperatively in patients with obesity, particularly those with renal or hepatic impairment, prolonged cardiopulmonary bypass or operative time, requiring vasopressor support, to prevent the deleterious effects of IAH.
Ultra-performance liquid chromatography for quantification of amphotericin B plasma concentrations after use of liposomal amphotericin B
Authors: Van Daele Ruth , de Beer Yvo , Croes Sander , Aarnoutse Rob , Wauters Joost , Maertens Johan , Spriet Isabel , Brüggemann Roger J
Published: December 2020

Objectives

Liposomal amphotericin B is widely used to treat life-threatening invasive fungal infections and has replaced conventional amphotericin B deoxycholate due to its more favourable toxicity profile. Despite the fact that liposomal amphotericin B has been licensed for several decades, there is still a paucity of clinical pharmacokinetic data. An assay for the quantification of amphotericin B is necessary to allow the study of its pharmacokinetics.

Methods

A UPLC-photodiode array (PDA) analytical method was developed and validated (linearity, accuracy, precision, dilution integrity, carry-over, selectivity and stability) in accordance with EMA requirements.

Results

The analytical method was validated over a concentration range of 0.5–50.0 mg/L. Accuracy ranged from 97.6% to 112.1% and within-day repeatability and between-day reproducibility from 1.0% to 6.6% and from 0.4% to 4.6%, respectively, dependent on the concentration. Originally, the goal was to develop an analytical method to separate the liposomal and free amphotericin B fractions, but this was not achieved. Difficulties and bottlenecks encountered are presented.

Conclusions

A UPLC-PDA analytical method was developed to quantify total amphotericin B in plasma after the use of liposomal amphotericin B.
Prospective evaluation of sentinel node navigation surgery in Japanese patients with low-risk endometrial cancer—safety and occurrence of lymphedema
Authors: Niikura Hitoshi , Toki Asami , Nagai Tomoyuki , Okamoto Satoshi , Shigeta Shogo , Tokunaga Hideki , Shimada Muneaki , Watanabe Mika , Yaegashi Nobuo
Published: December 2020

Objective

The present study aimed to clarify the occurrence rate of lymphedema and prognosis in patients with endometrial cancer according to sentinel lymph node biopsy alone with intraoperative histopathological examination.

Methods

The study included 45 consecutive patients with endometrial cancer treated at Tohoku University Hospital between October 2014 and August 2017. All patients had endometrial carcinoma with endometrioid histology Grade 1 or Grade 2 confirmed by biopsy and stage I on magnetic resonance imaging and/or computed tomography at their preoperative evaluation. Sentinel lymph node detection was performed by radioisotope and dye. Patients who were diagnosed intraoperatively as negative for sentinel lymph node metastasis did not undergo further systematic pelvic lymphadenectomy. The occurrence rate of lymphedema and prognosis was evaluated.

Results

Bilateral sentinel lymph nodes were detected in 44 of 45 patients (97%). Forty-three patients underwent sentinel lymph node biopsy alone, and only two patients underwent systematic lymphadenectomy. Sentinel lymph node metastases were detected in one patient intraoperatively and two patients postoperatively as ITCs. No patients experienced recurrence. New symptomatic lower-extremity lymphedema was identified in one of 43 patients (2.3%) who underwent sentinel lymph node biopsy alone.

Conclusion

Sentinel lymph node biopsy alone with intraoperative histopathological diagnosis appears to be a safe and effective strategy to detect lymph node metastasis and to reduce the number of patients with lower-extremity lymphedema among patients with endometrial cancer.
Haploinsufficiency of the TDP43 ubiquitin E3 ligase RNF220 leads to ALS-like motor neuron defects in the mouse
Authors: Ma Pengcheng , Li Yuwei , Wang Huishan , Mao Bingyu
Published: December 2020

TDP43 pathology is seen in a large majority of amyotrophic lateral sclerosis (ALS) cases, suggesting a central pathogenic role of this regulatory protein. Clarifying the molecular mechanism controlling TDP43 stability and subcellular location might provide important insights into ALS therapy. The ubiquitin E3 ligase RNF220 is involved in different neural developmental processes through various molecular targets in the mouse. Here, we report that the RNF220+/− mice showed progressively decreasing mobility to different extents, some of which developed typical ALS pathological characteristics in spinal motor neurons, including TDP43 cytoplasmic accumulation, atrocytosis, muscle denervation, and atrophy. Mechanistically, RNF220 interacts with TDP43 in vitro and in vivo and promotes its polyubiquitination and proteasomal degradation. In conclusion, we propose that RNF220 might be a modifier of TDP43 function in vivo and contribute to TDP43 pathology in neurodegenerative disease like ALS.
Fabrication of a liquid cell for in situ transmission electron microscopy
Authors: Li Xiaoguang , Mitsuishi Kazutaka , Takeguchi Masaki
Published: December 2020

Liquid cell transmission electron microscopy (LCTEM) enables imaging of dynamic processes in liquid with high spatial and temporal resolution. The widely used liquid cell (LC) consists of two stacking microchips with a thin wet sample sandwiched between them. The vertically overlapped electron-transparent membrane windows on the microchips provide passage for the electron beam. However, microchips with imprecise dimensions usually cause poor alignment of the windows and difficulty in acquiring high-quality images. In this study, we developed a new and efficient microchip fabrication process for LCTEM with a large viewing area (180 µm × 40 µm) and evaluated the resultant LC. The new positioning reference marks on the surface of the Si wafer dramatically improve the precision of dicing the wafer, making it possible to accurately align the windows on two stacking microchips. The precise alignment led to a liquid thickness of 125.6 nm close to the edge of the viewing area. The performance of our LC was demonstrated by in situ transmission electron microscopy imaging of the dynamic motions of 2-nm Pt particles. This versatile and cost-effective microchip production method can be used to fabricate other types of microchips for in situ electron microscopy.
Insidious presentation of intussusception with appendicitis
Authors: Ebrahimi Nargus , Yeh Yu-Ting
Published: December 2020

Intussusception in relation to appendicitis is an uncommon occurrence and is rarely described in the literature. We describe a case of diagnostic uncertainty and finding of ileocolic intussusception associated with appendicitis in a 22-year-old male. The patient presented with a history of acute right-sided abdominal pain. He underwent a computed tomography scan showing ileocolic intussusception following an operation with the finding of an inflamed appendix, which was likely to have served as a mechanical lead point of the intussusception. Due to the presence of ischaemia of the right colon, he underwent a right hemicolectomy.
Temporal lobe meningioma concurrent with multiple intracranial aneurysms
Authors: Wu Xia , Li Shun , Xie Chang-Li , Tang Xiaoping
Published: December 2020

Aneurysms in the internal carotid artery, specifically the ophthalmic artery segment, have a lower incidence than any other type of aneurysm. Cases showing simultaneous intracranial aneurysms and meningiomas are extremely rare. This report shares a case of an adult female diagnosed with a deep temporal lobe meningioma concurrent with bilateral internal carotid artery-ophthalmic segment aneurysms. One-stage surgery with coronal incisions and a right frontotemporal craniotomy was performed for this patient. The lesion was first removed along the tumor margin, and the anterior clinoid process was removed. The aneurysm was clipped using an aneurysm clip. The frontal lobe was lifted from the right side, the optic chiasm was separated, the left internal carotid artery was exposed and ophthalmic segment of the left internal carotid artery aneurysm was clipped using a combination of two cross-vessel clips.
Alternate bearing in fruit trees: fruit presence induces polar auxin transport in citrus and olive stem and represses IAA release from the bud
Authors: Haim Dor , Shalom Liron , Simhon Yasmin , Shlizerman Lyudmila , Kamara Itzhak , Morozov Michael , Albacete Alfonso , Rivero Rosa M , Sadka Avi
Published: December 2020

In many fruit trees, heavy fruit load in one year reduces flowering in the following year, creating a biennial fluctuation in yield termed alternate bearing (AB). In subtropical trees, where flowering induction is mostly governed by the accumulation of chilling hours, fruit load is thought to generate a signal (AB signal) that blocks the perception of cold induction. Fruit removal during a heavy-fruit-load year is effective at inducing flowering only if performed one to a few months before the onset of the flowering induction period. We previously showed that following fruit removal, the content of the auxin indoleacetic acid (IAA) in citrus buds is reduced, suggesting that the hormone plays a role in the AB signal. Here, we demonstrate that fruit presence generates relatively strong polar auxin transport in citrus and olive stems. Upon fruit removal, polar auxin transport is reduced and allows auxin release from the bud. Furthermore, using immunolocalization, hormone, and gene expression analyses, we show that in citrus, IAA level in the bud and specifically in the apical meristem is reduced upon fruit removal. Overall, our data provide support for the notion that fruit presence generates an auxin signal in the bud, which may affect flowering induction.
Renal SPECT/CT with 99mTc–dimercaptosuccinic acid is a non-invasive predictive marker for the development of interstitial fibrosis in a rat model of renal insufficiency
Authors: Bobot Mickaël , Hache Guillaume , Moyon Anaïs , Fernandez Samantha , Balasse Laure , Daniel Laurent , Garrigue Philippe , Brige Pauline , Chopinet Sophie , Dignat-George Françoise , Brunet Philippe , Burtey Stéphane , Guillet Benjamin
Published: December 2020

Background

Chronic kidney disease (CKD) increases cardiovascular risk and mortality. Renal fibrosis plays a major role in the progression of CKD but, to date, histology remains the gold standard to assess fibrosis. Non-invasive techniques are needed to assess renal parenchymal impairment and to perform the longitudinal evaluation of renal structure. Thus we evaluated renal isotopic imaging by single-photon emission computed tomography/computed tomography (SPECT/CT) with technetium-99m (99mTc)–dimercaptosuccinic acid (DMSA) to monitor renal impairment during renal insufficiency in rats.

Methods

Renal insufficiency was induced by an adenine-rich diet (ARD) at 0.25 and 0.5% for 28 days. Renal dysfunction was evaluated by assaying biochemical markers and renal histology. Renal parenchymal impairment was assessed by SPECT/CT isotopic imaging with 99mTc-DMSA on Days 0, 7, 14, 21, 28, 35 and 49.

Results

Compared with controls, ARD rats developed renal dysfunction characterized by increased serum creatinine and blood urea nitrogen, fibrosis and tubulointerstitial damage in the kidneys, with a dose-dependent effect of the adenine concentration. 99mTc-DMSA SPECT-CT imaging showed a significant decrease in renal uptake over time in 0.25 and 0.5% ARD rats compared with control rats (P = 0.011 and P = 0.0004, respectively). 99mTc-DMSA uptake on Day 28 was significantly inversely correlated with Sirius red staining evaluated on Day 49 (r = 0.89, P < 0.0001, R2 = 0.67).

Conclusions

99mTc-DMSA renal scintigraphy allows a longitudinal follow-up of risk of renal fibrosis in rats. We found that the reduction of renal parenchyma in ARD rats is inversely proportional to newly formed fibrous tissue in the kidney. Our results suggest that 99mTc-DMSA renal scintigraphy may be a useful non-invasive prognostic marker of the development of renal fibrosis in animals and should be tested in humans.
Outcome and molecular analysis of young children with choroid plexus carcinoma treated with non-myeloablative therapy: results from the SJYC07 trial
Authors: Liu Anthony P Y , Wu Gang , Orr Brent A , Lin Tong , Ashford Jason M , Bass Johnnie K , Bowers Daniel C , Hassall Tim , Fisher Paul G , Indelicato Daniel J , Klimo Paul , Boop Frederick , Conklin Heather , Onar-Thomas Arzu , Merchant Thomas E , Ellison David W , Gajjar Amar , Robinson Giles W
Published: December 2020

Background

Choroid plexus carcinoma (CPC) is a rare and aggressive tumor of infancy without a clear treatment strategy. This study describes the outcomes of children with CPC treated on the multi-institutional phase 2 SJYC07 trial and reports on the significance of clinical and molecular characteristics.

Methods

Eligible children <3 years-old with CPC were postoperatively stratified to intermediate-risk (IR) stratum if disease was localized or high-risk (HR) stratum, if metastatic. All received high-dose methotrexate–containing induction chemotherapy. IR-stratum patients received focal irradiation as consolidation whereas HR-stratum patients received additional chemotherapy. Consolidation was followed by oral antiangiogenic maintenance regimen. Survival rates and potential prognostic factors were analyzed.

Results

Thirteen patients (median age: 1.41 years, range: 0.21–2.93) were enrolled; 5 IR, 8 HR. Gross-total resection or near-total resection was achieved in ten patients and subtotal resection in 3. Seven patients had TP53-mutant tumors, including 4 who were germline carriers. Five patients experienced progression and died of disease; 8 (including 5 HR) are alive without progression. The 5-year progression-free survival (PFS) and overall survival rates were 61.5 ± 13.5% and 68.4 ± 13.1%. Patients with TP53-wild-type tumors had a 5-year PFS of 100% as compared to 28.6 ± 17.1% for TP53-mutant tumors (P = .012). Extent of resection, metastatic status, and use of radiation therapy were not significantly associated with survival.

Conclusions

Non-myeloablative high-dose methotrexate–containing therapy with maximal surgical resection resulted in long-term PFS in more than half of patients with CPC. TP53-mutational status was the only significant prognostic variable and should form the basis of risk-stratification in future trials.
Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Status in Decedents Undergoing Forensic Postmortem Examination in Maryland, May 24 to June 30, 2020
Authors: Althoff Keri N , Laeyendecker Oliver , Li Rong , Coburn Sally B , Klock Ethan , Baker Owen R , Quinn Thomas C , Michael Jeffrey , Shields Wendy C , Ehsani Johnathon , Thomas F Dennis , Graham Lindsey A , Ali Zabiullah , Manabe Yukari C , Li Ling
Published: December 2020

Seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies was 10% among the subset of decedents undergoing forensic postmortem examination in June in Maryland. Decedents of motor vehicle crashes had similar seroprevalence compared with those with a natural death (including decedents with SARS-CoV-2 infection). Decedents of motor vehicle crashes may be a sentinel surveillance population.
Minimal Population Prevalence and Mortality of Coronavirus Disease 2019 in Healthcare Personnel
Authors: Gupta Kalpana , Bellino Pamela , Samano Jazmin G , Strymish Judith , O’Brien William , Sprague Robert S , Charness Michael E
Published: December 2020

Among 3926 healthcare personnel in a multisite healthcare system, the minimal population prevalence of coronavirus disease 2019 (COVID-19) was 4.4% (bootstrap 95% confidence interval [CI], 3.7%–5.0%), and the infection fatality rate was 0.6% (bootstrap 95% CI, 0.0%–1.7%). Rates reflected both local community prevalence and hospital exposures but not specifically exposure on COVID-19 units.