bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Mutation of HINT1 Gene in an Adolescent Female with Axonal Neuropathy and Neuromyotonia
Authors: Kara Bülent , Gül Sedat , Güneş Ayfer Sakarya , Mülayim Serap , Yeşil Gözde
Published: May 2020

HINT1 gene mutations cause an axonal neuropathy with some specific findings including presence of neuromyotonia, autosomal recessive inheritance, onset in the first decade, and primary motor involvement. In this case report, we described an 18-year-old female patient who presented to the clinic with gait instability and muscle stiffness. A homozygous novel c.180_181delAT (p.Ser61Profs*8) variant in the HINT1 gene was found by clinical exome analysis. Parents were heterozygous for the same variant. The patient was diagnosed with autosomal recessive axonal neuropathy with neuromyotonia. The presence of neuromyotonia must be evaluated in patients with hereditary axonal neuropathies as this can help the diagnosis prior to genetic testing.
Stereotactic Body Radiation Therapy for Hepatocellular Carcinoma
Authors: Campbell Shauna R. , Smile Timothy D. , Sittenfeld Sarah M.C. , Stephans Kevin L.
Published: May 2020

Primary liver cancer is the seventh most common cancer worldwide and is the second leading cause of cancer-related death. Hepatocellular carcinoma (HCC) accounts for three-quarters of primary liver cancers and less than a third of patients present with curable disease. Liver-directed therapy is essential for the treatment of patients with unresectable HCC and the advancement of stereotactic body radiation therapy (SBRT) has made radiation a safe and effective treatment option in a range of clinical presentations. In this review, we discuss the technical aspects of SBRT and the general approach to treatment of HCC. We explore the use of SBRT for bridging to transplant, downstaging, and the treatment of large tumors and portal vein tumor thrombus. Although there is limited high-quality randomized data, we review the evidence comparing SBRT with other liver-directed therapies and explore areas for future investigation.
The Macrophage Responses during Diabetic Oral Ulcer Healing by Liquid Coconut Shell Smoke: An Immunohistochemical Analysis
Authors: Surboyo Meircurius Dwi Condro , Mahdani Fatma Yasmin , Ernawati Diah Savitri , Sarasati Andari , Rezkita Fianza
Published: May 2020

Objectives Liquid coconut shell smoke (LC-SS) is used in natural food preservation for a long history. The purpose of this study was to analyze the role of LC-SS in macrophage responses during diabetic oral ulcer healing as medication.

Materials and Methods Oral ulcers were induced in the labial lower mucosa of the research subjects using a round steel blade following diabetic induction by means of alloxan. Twenty-four diabetic Wistar rats presenting oral ulcers were divided into two groups, a test group, which was given topical treatment of LC-SS and a control group, which was given benzydamine hydrochloride (BHCl). The role of LC-SS in macrophages was assessed by means of immunohistochemistry for nuclear factor kappa B (NF-κB) and tumor necrosis factor-α (TNF-α) expression.

Result LC-SS increased macrophages compared with BHCl (p = 0.000). The LC-SS affected only TNF-α expression by stimulating NF-κB expression (p = 0.046) but did not macrophage numbers (p = 0.861).

Conclusion LC-SS has a stronger effect compared with BHCl on diabetic oral ulcer healing by increasing macrophage response to produce TNF-α while decreasing NF-κB expression.
Effects of Hydrogen Bonding on the Rotational Dynamics of Water-Like Molecules in Liquids: Insights from Molecular Dynamics Simulations
Authors: Madhavi W. A. Monika , Weerasinghe Samantha , Momot Konstantin I.
Published: May 2020

Rotational motion of molecules plays an important role in determining NMR spin relaxation properties of liquids. The textbook theory of NMR spin relaxation predominantly uses the assumption that the reorientational dynamics of molecules is described by a continuous time rotational diffusion random walk with a single rotational diffusion coefficient. Previously we and others have shown that reorientation of water molecules on the timescales of picoseconds is not consistent with the Debye rotational-diffusion model. In particular, multiple timescales of molecular reorientation were observed in liquid water. This was attributed to the hydrogen bonding network in water and the consequent presence of collective rearrangements of the molecular network. In order to better understand the origins of the complex reorientational behaviour of water molecules, we carried out molecular dynamics (MD) simulations of a liquid that has a similar molecular geometry to water but does not form hydrogen bonds: hydrogen sulfide. These simulations were carried out at T=208K and p=1 atm (~5K below the boiling point). Ensemble-averaged Legendre polynomial functions of hydrogen sulfide exhibited a Gaussian decay on the sub-picosecond timescale but, unlike water, did not exhibit oscillatory behaviour. We attribute these differences to hydrogen sulfide’s absence of hydrogen bonding.
Diversity and population genetic structure of Octopus hubbsorum in the Mexican Pacific inferred from mitochondrial DNA sequences
Authors: Dueñas-Romero José de Jesús , Granados-Amores Jasmín , Palacios-Salgado Deivis Samuel , Domínguez-Contreras José Francisco , Flores-Ortega Juan Ramón , García-Rodríguez Francisco Javier
Published: May 2020

Octopus hubbsorum is the most commonly captured species of octopus on the western coast of Mexico. Despite the commercial importance of this species, management information remains scarce. We determined the genetic diversity and population genetic structure of O. hubbsorum by using mtDNA sequences (COI and ND5). The population structure was not supported by AMOVA or a spatial clustering model. Furthermore, an isolation by distance model did not explain our data. Three haplogroups were detected using a Bayesian assignment; however, the distribution of these haplogroups did not differ among the sampling sites. Our results indicated historical processes of a sudden population expansion, as has been reported for other species in the study region as consequence of climatic changes. However, this expansion did not affect the distribution of the mitochondrial lineages analysed in the study. The weak population genetic structure in O. hubbsorum associated with the life history of the species can explain our results. We suggest that to expand knowledge regarding the genetic structure and population dynamics of O. hubbsorum throughout its range, markers such as microsatellites or single-nucleotide polymorphisms (SNPs) are needed. Thus, on the basis of the information available, the studied population should be assumed to have a weak genetic structure.
First report of nymphs of the introduced pentastomid, Linguatula serrata, in red-necked wallabies (Notamacropus rufogriseus) in Australia
Authors: Barton Diane P. , Porter Megan , Baker Ashleigh , Zhu Xiaocheng , Jenkins David J. , Shamsi Shokoofeh
Published: May 2020

The presence of nymphs of the introduced pentastomid parasite Linguatula serrata is verified in a native Australian animal, the red-necked wallaby (Notamacropus rufogriseus), for the first time. Morphological and genetic analyses confirmed the species identification, with a 100% genetic match to samples collected from various introduced animals from the same location in Kosciuszko National Park. Previous reports of pentastomids, including possible Linguatula sp. infections, in native animals are discussed. More research is required to confirm the validity of these reports.
Case(mis)matching in German free relative clauses in the self-paced reading paradigm
Authors: Mewe Jana
Published: May 2020

Off-line measures suggest that the hierarchy rule strategy applies to the processing of free relative clauses (RCs) in German, suggesting that case matches between covert head and RC-pronoun are preferred, whereas mismatches are dissociated based on their (non)conformity with the case hierarchy. We asked whether on-line sentence processing supports this pattern, and investigated free RCs with combinations of nominative, accusative and dative case in the self-paced reading paradigm. Our results are captured best by assuming two further strategies: the parallel syntactic function strategy and, especially, the subject-first strategy. Based on these strategies, we provide an Optimality Theory-style analysis that explains prior findings and particularities of incremental sentence processing, and that additionally accounts for the exceptional behaviour of accusative-nominative mismatches.
Priming paradigmatic gaps
Authors: Vea Joakim Andreassen , Johansson Christer
Published: May 2020

We present an experimental study on paradigmatic gaps in the neuter gender of Norwegian adjectives. The formation of neuter gender forms is typically not complicated, and yet people hesitate to use a predictable set of adjectives. We investigate the effect of priming in order to determine if the missing neuter forms will facilitate lexical decisions for their common gender form, possibly through lemma activation. A clear difference was found between regular and problematic adjectives. This shows that the intuition of speakers is reflected in detectable differences in processing.
A good-enough representation is not good enough
Authors: Koring Loes
Published: May 2020

It has been proposed that language processing invokes extra-grammatical heuristics in addition to, or instead of the computational system (e.g., Townsend & Bever, 2001; Karimi & Ferreira, 2016). The outputs of these extra-grammatical heuristics are called “good-enough” representations. These representations lack (syntactic) detail and are incomplete (Karimi & Ferreira, 2016). This paper evaluates this claim by investigating one extra-grammatical processing heuristic in particular: the NV(N)-strategy. Two experiments prove that (i) interpretations that would result from application of the NV(N)-strategy are sometimes difficult to generate and (ii) listeners compute (syntactic) representations for sentences that are more detailed than the NV(N)-strategy would predict. This gives rise to the question whether “good-enough” representations are computed at all.
A syntactically based treatment of relative clauses
Authors: D’Ortenzio Silvia , Montino Silvia , Martini Alessandro , Trevisi Patrizia , Volpato Francesca
Published: May 2020

In this paper, we describe three case studies of a syntactic intervention given to three Italian-speaking children with cochlear implants (CIs) to improve proficiency in the production and comprehension of relative clauses, and also their narrative skills. The methodology adopted for the syntactic intervention follows previous studies on aphasic patients with agrammatism and children with developmental language disorders (DLD). Indeed, these studies have shown that an explicit teaching of syntactic rules helps in the recovery and improvement of complex structures derived by syntactic movement. Results showed a general improvement in the production and comprehension of relative clauses, and generalization effects to untrained structures. Moreover, also narrative skills improved. Results were maintained several months after the end of the syntactic intervention.
Understanding stancetaking through gestures and linguistic practices in a
public political debate in Hong Kong
Authors: Wan Helen
Published: May 2020

Hong Kong has enjoyed partial universal suffrage in both
District Council election as well as the Legislative Council election since the
handover in 1997. This paper looks into the 2016 Hong Kong Legislative Council
electoral debate with the combination of discourse analysis using the Stance
Triangle (Du Bois 2007) and
gesture-unit analysis (Kendon 2004) to
study how verbal and non-verbal activities are being strategically organized to
project both affective and epistemic stances by the elected incumbent, Alvin
Yeung, and his opponents. The findings suggest Cantonese utterance final particles
and gestures are strategically and aptly employed to achieve both expressive and
communicative purposes in the political debates where they can not only elucidate
their policy agenda but also defeat the opponents and win the votes.
Impact of power relations on news translation in China
Authors: Xia Liang
Published: May 2020

Global news transmission relies on language and particularly
on the services of translation. Decision making exists in every step of the
translation process, for instance, from the text selection to the discursive
expression, and from information transference to culture communication. This study
examines the translation practice of news in Cankao Xiaoxi
(Chinese: 参考消息), the most read Chinese daily run by the Chinese
government that collects various news or information from international media,
translates and reprints them in Chinese. This study outlines various powers that
underline text manipulation in this state news agency and explores the impact of
power relations on both the process and the product of news translation. Combining
an ethnographic approach with a critical discourse analysis of news translation,
this study investigates the institutional contexts and human agencies involved in
the news making process, which lead to the manipulation of the news production.
This study reveals that various powers determine how to shape the already shaped
news via translating and that network of power relations underlying news
translation in China is hierarchical. This hierarchy of power relations affords
both macro and micro-analytical perspectives on the realisation of manipulation in
news translation in China.
Identification of the putative N-acetylglucosaminidase CseA associated with daughter cell separation in Tetragenococcus halophilus
Authors: Shirakawa Daichi , Wakinaka Takura , Watanabe Jun
Published: May 2020

The lactic acid bacterium Tetragenococcus halophilus, which is used as a starter to brew soy sauce, comprises both cluster-forming strains and dispersed strains. The cluster-forming strains are industrially useful for obtaining clear soy sauce, because the cell clusters are trapped by filter cloth when the soy sauce mash is pressed. However, the molecular mechanism underlying cell cluster formation is unknown. Whole genome sequence analysis and subsequent target sequence analysis revealed that the cluster-forming strains commonly have functional defects in N-acetylglucosaminidase CseA, a peptidoglycan hydrolase. CseA is a multimodular protein that harbors a GH73 domain and six peptidoglycan-binding LysM domains. Recombinant CseA hydrolyzed peptidoglycan and promoted cell separation. Functional analysis of truncated CseA derivatives revealed that the LysM domains play an important role in efficient peptidoglycan degradation and cell separation. Taken together, the results of this study identify CseA as a factor that greatly affects the cluster formation in T. halophilus.
Inhibition kinetics of acetosyringone on xylanase in hydrolysis of hemicellulose
Authors: Liu Feng , Xu Wen-Fei , Mu Hang , Lv Zhi-Rong , Peng Jie , Guo Chao , Zhou Hai-Meng , Ye Zhuo-Ming , Li Xu-Hui
Published: May 2020

Many phenolic compounds, derived from lignin during the pretreatment of lignocellulosic biomass, could obviously inhibit the activity of cellulolytic and hemicellulolytic enzymes. Acetosyringone (AS) is one of the phenolic compounds produced from lignin degradation. In this study, we investigated the inhibitory effects of AS on xylanase activity through kinetic experiments. The results showed that AS could obviously inhibit the activity of xylanase in a reversible and noncompetitive binding manner (up to 50% activity loss). Inhibitory kinetics and constants of xylanase on AS were conducted by the HCH-1 model (β = 0.0090 ± 0.0009 mM−1). Furthermore, intrinsic and 8-anilino-1-naphthalenesulfonic (ANS)-binding fluorescence results showed that the tertiary structure of AS-mediated xylanase was altered. These findings provide new insights into the role of AS in xylanase activity. Our results also suggest that AS was an inhibitor of xylanase and targeting AS was a potential strategy to increase xylose production.
Changes in muscle strength and physical function in older patients during and after hospitalisation: a prospective repeated-measures cohort study
Authors: Hartley Peter , Romero-Ortuno Roman , Wellwood Ian , Deaton Christi
Published: May 2020

Aim

to investigate changes in knee-extension strength and physical function in older adults during and after acute hospital admission, and the contributions of illness severity, frailty and sedentary activity to changes in knee-extension strength.

Methods

prospective repeated-measures cohort study on a sample of participants aged ≥75 recruited within 24 hours of acute hospital admission. Knee-extension, grip strength and functional mobility (de Morton Mobility Index, DEMMI) were measured at recruitment, day 7 (or discharge if earlier), and at follow-up 4–6 weeks later. During the first 7 days, continuous measurement of physical activity and daily measurements of muscle strength were taken. Participants recalled the functional ability they had 2-weeks before admission and self-reported it at follow-up (Barthel Index, BI).

Results

sixty-five of 70 participants (median age 84 years) had at least one repeated measure of muscle strength in hospital. Knee-extension strength declined during hospitalisation by 11% (P < 0.001), but did not change post-hospitalisation (P = 0.458). Grip strength did not change during hospitalisation (P = 0.665) or from discharge to follow-up (P = 0.508). General functional ability (BI) deteriorated between 2 weeks before admission and follow-up (P < 0.001). Functional mobility (DEMMI) improved during hospitalisation (P < 0.001), but did not change post-hospitalisation (P = 0.508). A repeated-measures mixed model showed that greater loss in knee-extension strength during hospitalisation was associated with increased sedentary time, frailty and baseline strength and lower baseline inflammatory levels.

Conclusions

our observations add to a growing body of evidence on potential risk factors for hospital-associated deconditioning.
Privacy, Literature, and Public Discourse
Authors: Rosen David , Santesso Aaron
Published: May 2020

In the last few decades, something has changed about how Americans conceive of privacy, which has had consequences for how writers address their publics: how writers write. This essay argues that rapidly evolving and expanding surveillance regimes have profoundly affected our sense of where the private life begins and ends and what can or cannot be concealed from others. Discourses characterized by fragmentation, opacity, and indirection have become both a means by which we communicate information about ourselves to the larger world and a mimetic representation of how that surveillance-mediated world often appears to us. Literature has played a crucial role in these transformations and has served as a laboratory for many of these emerging discourses. This essay focuses on two recent and contrasting cohorts of American writers: a slightly older group of authors who saw the sacrifice of individual privacy as having catastrophic implications for liberal democracy, and a younger group whose views of privacy and communication were, on the whole, less panicked and more tactical. The essay concludes by considering what happens when rhetorical modes meant primarily to preserve the private self reenter the public sphere and assert themselves within a civil-minded conversation.
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy
Authors: Xie Ruopeng , Li Jiahui , Wang Jiawei , Dai Wei , Leier André , Marquez-Lago Tatiana T , Akutsu Tatsuya , Lithgow Trevor , Song Jiangning , Zhang Yanju
Published: May 2020

Virulence factors (VFs) enable pathogens to infect their hosts. A wealth of individual, disease-focused studies has identified a wide variety of VFs, and the growing mass of bacterial genome sequence data provides an opportunity for computational methods aimed at predicting VFs. Despite their attractive advantages and performance improvements, the existing methods have some limitations and drawbacks. Firstly, as the characteristics and mechanisms of VFs are continually evolving with the emergence of antibiotic resistance, it is more and more difficult to identify novel VFs using existing tools that were previously developed based on the outdated data sets; secondly, few systematic feature engineering efforts have been made to examine the utility of different types of features for model performances, as the majority of tools only focused on extracting very few types of features. By addressing the aforementioned issues, the accuracy of VF predictors can likely be significantly improved. This, in turn, would be particularly useful in the context of genome wide predictions of VFs. In this work, we present a deep learning (DL)-based hybrid framework (termed DeepVF) that is utilizing the stacking strategy to achieve more accurate identification of VFs. Using an enlarged, up-to-date dataset, DeepVF comprehensively explores a wide range of heterogeneous features with popular machine learning algorithms. Specifically, four classical algorithms, including random forest, support vector machines, extreme gradient boosting and multilayer perceptron, and three DL algorithms, including convolutional neural networks, long short-term memory networks and deep neural networks are employed to train 62 baseline models using these features. In order to integrate their individual strengths, DeepVF effectively combines these baseline models to construct the final meta model using the stacking strategy. Extensive benchmarking experiments demonstrate the effectiveness of DeepVF: it achieves a more accurate and stable performance compared with baseline models on the benchmark dataset and clearly outperforms state-of-the-art VF predictors on the independent test. Using the proposed hybrid ensemble model, a user-friendly online predictor of DeepVF (http://deepvf.erc.monash.edu/) is implemented. Furthermore, its utility, from the user’s viewpoint, is compared with that of existing toolkits. We believe that DeepVF will be exploited as a useful tool for screening and identifying potential VFs from protein-coding gene sequences in bacterial genomes.
DeepLGP: a novel deep learning method for prioritizing lncRNA target genes
Authors: Zhao Tianyi , Hu Yang , Peng Jiajie , Cheng Liang
Published: May 2020

Motivation

Although long non-coding RNAs (lncRNAs) have limited capacity for encoding proteins, they have been verified as biomarkers in the occurrence and development of complex diseases. Recent wet-lab experiments have shown that lncRNAs function by regulating the expression of protein-coding genes (PCGs), which could also be the mechanism responsible for causing diseases. Currently, lncRNA-related biological data are increasing rapidly. Whereas, no computational methods have been designed for predicting the novel target genes of lncRNA.

Results

In this study, we present a graph convolutional network (GCN) based method, named DeepLGP, for prioritizing target PCGs of lncRNA. First, gene and lncRNA features were selected, these included their location in the genome, expression in 13 tissues and miRNA-mediated lncRNA–gene pairs. Next, GCN was applied to convolve a gene interaction network for encoding the features of genes and lncRNAs. Then, these features were used by the convolutional neural network for prioritizing target genes of lncRNAs. In 10-cross validations on two independent datasets, DeepLGP obtained high area under curves (0.90–0.98) and area under precision-recall curves (0.91–0.98). We found that lncRNA pairs with high similarity had more overlapped target genes. Further experiments showed that genes targeted by the same lncRNA sets had a strong likelihood of causing the same diseases, which could help in identifying disease-causing PCGs.

Availability and implementation

https://github.com/zty2009/LncRNA-target-gene.

Supplementary information

Supplementary data are available at Bioinformatics online.
AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data
Authors: Whalen Andrew , Gorjanc Gregor , Hickey John M
Published: May 2020

AlphaFamImpute is an imputation package for calling, phasing and imputing genome-wide genotypes in outbred full-sib families from single nucleotide polymorphism (SNP) array and genotype-by-sequencing (GBS) data. GBS data are increasingly being used to genotype individuals, especially when SNP arrays do not exist for a population of interest. Low-coverage GBS produces data with a large number of missing or incorrect naïve genotype calls, which can be improved by identifying shared haplotype segments between full-sib individuals. Here, we present AlphaFamImpute, an algorithm specifically designed to exploit the genetic structure of full-sib families. It performs imputation using a two-step approach. In the first step, it phases and imputes parental genotypes based on the segregation states of their offspring (i.e. which pair of parental haplotypes the offspring inherited). In the second step, it phases and imputes the offspring genotypes by detecting which haplotype segments the offspring inherited from their parents. With a series of simulations, we find that AlphaFamImpute obtains high-accuracy genotypes, even when the parents are not genotyped and individuals are sequenced at <1x coverage.

Availability and implementation

AlphaFamImpute is available as a Python package from the AlphaGenes website http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute.

Supplementary information

Supplementary data are available at Bioinformatics online.
bGWAS: an R package to perform Bayesian genome wide association studies
Authors: Mounier Ninon , Kutalik Zoltán
Published: May 2020

Increasing sample size is not the only strategy to improve discovery in Genome Wide Association Studies (GWASs) and we propose here an approach that leverages published studies of related traits to improve inference. Our Bayesian GWAS method derives informative prior effects by leveraging GWASs of related risk factors and their causal effect estimates on the focal trait using multivariable Mendelian randomization. These prior effects are combined with the observed effects to yield Bayes Factors, posterior and direct effects. The approach not only increases power, but also has the potential to dissect direct and indirect biological mechanisms.

Availability and implementation

bGWAS package is freely available under a GPL-2 License, and can be accessed, alongside with user guides and tutorials, from https://github.com/n-mounier/bGWAS.

Supplementary information

Supplementary data are available at Bioinformatics online.
Eocene palms from central Myanmar in a South-East Asian and global perspective: evidence from the palynological record
Authors: Huang Huasheng , Morley Robert , Licht Alexis , Dupont-Nivet Guillaume , Grímsson Friðgeir , Zetter Reinhard , Westerweel Jan , Win Zaw , Wa Aung Day , Hoorn Carina
Published: May 2020

In the Palaeogene, pollen assemblages at low and mid latitudes are characterized by abundant palm and palm-like (PPL) taxa. Although these taxa have been widely reported, their occurrence in the Palaeogene of Myanmar remains poorly documented. Here we report on the morphology of PPL pollen along a middle to upper Eocene sedimentary sequence in central Myanmar and discuss their nearest living relatives (NLRs). Principal components analysis (PCA) indicates that Palmaepollenites kutchensis, Dicolpopollis and Longapertites were dispersed from freshwater plants, whereas the parent taxon of Proxapertites operculatus was probably a member of the coastal vegetation in the manner of Spinizonocolpites. This, with sedimentological data, suggests a palaeoenvironmental change from a brackish, tidally influenced environment to a fully freshwater setting through the late Eocene. Additionally, we mapped and compared the geographical distribution of selected Eocene palm taxa and their NLRs, and found that their distributions shrank after the Eocene. Moreover, in the Palaeogene, species diversity of selected PPL taxa seems lower in Myanmar than in the Indian subcontinent and other regions in South-East Asia. We hypothesize that in the Eocene the Indo–Asian collision zone formed a ‘hotspot’ for palm diversity, which is reflected in species-rich palynofloras. However, the local palm diversity declined after the Eocene, whereas, at the global level, palm distribution was distinctly reduced between the Eocene and the present. We propose that the retreat of the palms may have occurred as early as the Eocene – Oligocene Transition (EOT), but this remains to be confirmed by the study of EOT pollen records in tropical regions.
Personalized Nutrition for Inflammatory Bowel Disease
Authors: Collins Colm B , Roche Helen M
Published: May 2020

Lay Summary

A person’s diet may impact inflammatory bowel disease (IBD) risk. IBD is an inflammatory condition. We explore how certain foods may trigger, or indeed attenuate, inflammation in some IBD patients, but not others. Greater knowledge is needed underpinning personalized nutrition within effective medical management.
GTDB: an integrated resource for glycosyltransferase sequences and annotations
Authors: Zhou Chenfen , Xu Qingwei , He Sheng , Ye Wei , Cao Ruifang , Wang Pengyu , Ling Yunchao , Yan Xing , Wang Qingzhong , Zhang Guoqing
Published: May 2020

Glycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natural products with pharmaceutical or agrochemical values. Here, we first collected comprehensive information on GTs, including amino acid sequences, coding region sequences, available tertiary structures, protein classification families, catalytic reactions and metabolic pathways. Then, we developed sequence search and molecular docking processes for GTs, resulting in a GTs database (GTDB). In the present study, 520 179 GTs from approximately 21 647 species that involved in 394 kinds of different reactions were deposited in GTDB. GTDB has the following useful features: (i) text search is provided for retrieving the complete details of a query by combining multiple identifiers and data sources; (ii) a convenient browser allows users to browse data by different classifications and download data in batches; (iii) BLAST is offered for searching against pre-defined sequences, which can facilitate the annotation of the biological functions of query GTs; and lastly, (iv) GTdock using AutoDock Vina performs docking simulations of several GTs with the same single acceptor and displays the results based on 3Dmol.js allowing easy view of models.
Influence of prosthesis-related factors on the occurrence of early leaflet thrombosis after transcatheter aortic valve implantation
Authors: Breitbart Philipp , Pache Gregor , Minners Jan , Hein Manuel , Schröfel Holger , Neumann Franz-Josef , Ruile Philipp
Published: May 2020

Aims

Early leaflet thrombosis (LT) is a well-described phenomenon after transcatheter aortic valve implantation (TAVI) with an incidence around 15%. Data about predictors of LT are scarce. The purpose of the study was to investigate the influence of prosthesis-related factors on the occurrence of LT.

Materials and results

Fusion imaging of pre- and post-procedural computed tomography angiography was performed in 55 TAVI patients with LT and 140 selected patients as control groups (85 patients in an unmatched and 55 in a matched control) to obtain a 3D reconstruction of the transcatheter heart valve (THV) within the native annulus region. All patients received a balloon-expandable Sapien 3 THV. The THV length above and below the native annulus was measured within the fused images to assess the implantation depth. The deployed THV area was quantified on three heights (left ventricular outflow tract end, stent centre, and aortic end) to determine the average expansion of the prosthesis as percent of the nominal area. We also calculated the extent of prosthesis waist in percent of maximum area. After multivariate adjustment, the extent of THV waist [odds ratio (OR) per 10% (confidence interval, CI) 0.636 (0.526–0.769), P < 0.001] as prosthesis-related factor and previous oral anticoagulation [OR (CI) 0.070 (0.020–0.251), P < 0.001] had significant, independent influence on the occurrence of LT. The implantation depth showed no influence on LT manifestation (P = 0.704).

Conclusion

Besides the absence of previous oral anticoagulation, a less pronounced waist of the implanted THV was a prosthesis-position-related independent predictor of LT after TAVI using the Sapien 3.
Unreliable Protection: An Experimental Study of Experts’ In Bello Proportionality Decisions
Authors: Statman Daniel , Sulitzeanu-Kenan Raanan , Mandel Micha , Skerker Michael , de Wijze Stephen
Published: May 2020

The proportionality principle is an international humanitarian law requirement intended to constrain the use of military force in order to protect civilians in armed conflicts. This research experimentally assesses the reliability of its application by legal and moral experts (in 11 countries), by military officers (in two countries) and by laypeople. Reliability was evaluated according to three criteria: inter-expert convergence; sensitivity to relevant factors; and robustness – relative (lack of) susceptibility to biases. Unlike laypeople, experts and military officers performed well on the sensitivity criterion and manifested an appropriate understanding of the principle at the abstract level. However, both groups of experts failed to reach reasonable judgment convergence. These findings cast doubt on the reliability of the protection provided to civilians during warfare, even when warring parties attempt to abide by the proportionality principle.
Acute and mid-term outcome of ethanol infusion of vein of Marshall for the treatment of perimitral flutter
Authors: Takigawa Masateru , Vlachos Konstantinos , Martin Claire A , Bourier Felix , Denis Arnaud , Kitamura Takeshi , Cheniti Ghassen , Lam Anna , Martin Ruairidh , Frontera Antonio , Thompson Nathaniel , Massoullié Grégoire , Wolf Michael , Escande William , André Clémentine , Zeng Li-Jun , Nakatani Yosuke , Nakashima Takashi , Pillois Xavier , Ramirez Daniel , Duchateau Josselin , Pambrun Thomas , Sacher Frederic , Cochet Hubert , Hocini Mélèze , Haïssaguerre Michel , Jaïs Pierre , Derval Nicolas
Published: May 2020

Aims 

We hypothesized that an epicardial approach using ethanol infusion in the vein of Marshall (EIVOM) may improve the result of ablation for perimitral flutter (PMF).

Methods and results 

We studied 103 consecutive patients with PMF undergoing high-resolution mapping. The first 71 were treated with radiofrequency (RF) ablation alone (RF-group), and the next 32 underwent EIVOM followed by RF on the endocardial and epicardial mitral isthmus (EIVOM/RF-group). Contact force was not measured during ablation. Acute and 1-year outcomes were compared. Flutter termination rates were similar between the RF-group (63/71, 88.7%) and EIVOM/RF-group (31/32, 96.8%, P = 0.27). Atrial tachycardia (AT) terminated with EIVOM alone in 22/32 (68.6%) in the EIVOM/RF-group. Bidirectional block of mitral isthmus was always achieved in the EIVOM/RF-group, but significantly less frequently achieved in the RF-group (62/71, 87.3%; P = 0.05). Median RF duration for AT termination/conversion was shorter [0 (0–6) s in the EIVOM/RF-group than 312 (55–610) s in the RF-group, P < 0.0001], as well as for mitral isthmus block in the EIVOM/RF-group [246 (0–663) s] than in the RF-group [900 (525–1310) s, P < 0.0001]. Pericardial effusion was observed in 1/32 (3.2%) in EIVOM/RF-group and 5/71 (7.0%) in RF-group (P = 0.66); two in RF-group required drainage and one of them developed subsequent ischaemic stroke. One-year follow-up demonstrated fewer recurrences in the EIVOM/RF-group [6/32 (18.8%)] than in the RF-group [29/71 (40.8%), P = 0.04]. By multivariate analysis, only EIVOM was significantly associated with less AT recurrence (hazard ratio = 0.35, P = 0.018).

Conclusion 

Ethanol infusion in the vein of Marshall may reduce RF duration required for PMF termination as well as for mitral isthmus block without severe complications, and the mid-term outcome may be improved by this approach.
Remote monitoring of cardiac implanted electronic devices: legal requirements and ethical principles - ESC Regulatory Affairs Committee/EHRA joint task force report
Authors: Nielsen Jens Cosedis , Kautzner Josef , Casado-Arroyo Ruben , Burri Haran , Callens Stefaan , Cowie Martin R , Dickstein Kenneth , Drossart Inga , Geneste Ginger , Erkin Zekeriya , Hyafil Fabien , Kraus Alexander , Kutyifa Valentina , Marin Eduard , Schulze Christian , Slotwiner David , Stein Kenneth , Zanero Stefano , Heidbuchel Hein , Fraser Alan G
Published: May 2020

The European Union (EU) General Data Protection Regulation (GDPR) imposes legal responsibilities concerning the collection and processing of personal information from individuals who live in the EU. It has particular implications for the remote monitoring of cardiac implantable electronic devices (CIEDs). This report from a joint Task Force of the European Heart Rhythm Association and the Regulatory Affairs Committee of the European Society of Cardiology (ESC) recommends a common legal interpretation of the GDPR. Manufacturers and hospitals should be designated as joint controllers of the data collected by remote monitoring (depending upon the system architecture) and they should have a mutual contract in place that defines their respective roles; a generic template is proposed. Alternatively, they may be two independent controllers. Self-employed cardiologists also are data controllers. Third-party providers of monitoring platforms may act as data processors. Manufacturers should always collect and process the minimum amount of identifiable data necessary, and wherever feasible have access only to pseudonymized data. Cybersecurity vulnerabilities have been reported concerning the security of transmission of data between a patient’s device and the transceiver, so manufacturers should use secure communication protocols. Patients need to be informed how their remotely monitored data will be handled and used, and their informed consent should be sought before their device is implanted. Review of consent forms in current use revealed great variability in length and content, and sometimes very technical language; therefore, a standard information sheet and generic consent form are proposed. Cardiologists who care for patients with CIEDs that are remotely monitored should be aware of these issues.
Enhanced microbial degradation of irradiated cellulose under hyperalkaline conditions
Authors: Bassil Naji M , Small Joe S , Lloyd Jonathan R
Published: May 2020

Intermediate-level radioactive waste includes cellulosic materials, which under the hyperalkaline conditions expected in a cementitious geological disposal facility (GDF) will undergo abiotic hydrolysis forming a variety of soluble organic species. Isosaccharinic acid (ISA) is a notable hydrolysis product, being a strong metal complexant that may enhance the transport of radionuclides to the biosphere. This study showed that irradiation with 1 MGy of γ-radiation under hyperalkaline conditions enhanced the rate of ISA production from the alkali hydrolysis of cellulose, indicating that radionuclide mobilisation to the biosphere may occur faster than previously anticipated. However, irradiation also made the cellulose fibres more available for microbial degradation and fermentation of the degradation products, producing acidity that inhibited ISA production via alkali hydrolysis. The production of hydrogen gas as a fermentation product was noted, and this was associated with a substantial increase in the relative abundance of hydrogen-oxidising bacteria. Taken together, these results expand our conceptual understanding of the mechanisms involved in ISA production, accumulation and biodegradation in a biogeochemically active cementitious GDF.
Comparative Transcriptomics across Nematode Life Cycles Reveal Gene Expression Conservation and Correlated Evolution in Adjacent Developmental Stages
Authors: Lu Min R , Lai Cheng-Kuo , Liao Ben-Yang , Tsai Isheng Jason
Published: May 2020

Nematodes are highly abundant animals with diverse habitats and lifestyles. Some are free living whereas others parasitize animals or plants, and among the latter, infection abilities change across developmental stages to infect hosts and complete life cycles. To determine the relationship between transcriptome evolution and morphological divergences among nematodes, we compared 48 transcriptomes of different developmental stages across eight nematode species. The transcriptomes were clustered broadly into embryo, larva, and adult stages, with the developmental plastic stages were separated from common larval stages within the larval branch. This suggests that development was the major determining factor after lifestyle changes, such as parasitism, during transcriptome evolution. Such patterns were partly accounted for by tissue-specific genes—such as those in oocytes and the hypodermis—being expressed at different proportions. Although nematodes typically have 3–5 larval stages, the transcriptomes for these stages were found to be highly correlated within each species, suggesting high similarity among larval stages across species. For the Caenorhabditis elegans–Caenorhabditis briggsae and Strongyloides stercoralis–Strongyloides venezuelensis comparisons, we found that ∼50% of genes were expressed at multiple stages, whereas half of their orthologs were also expressed in multiple but different stages. Such frequent changes in expression have resulted in concerted transcriptome evolution across adjacent stages, thus generating species-specific transcriptomes over the course of nematode evolution. Our study provides a first insight into the evolution of nematode transcriptomes beyond embryonic development.
Cross-border medical travels from Cambodia: pathways to care, associated costs and equity implications
Authors: Liverani Marco , Ir Por , Jacobs Bart , Asante Augustine , Jan Stephen , Leang Supheap , Man Nicola , Hayen Andrew , Wiseman Virginia
Published: May 2020

In low- and middle-income countries, patients may travel abroad to seek better health services or treatments that are not available at home, especially in regions where great disparities exist between the standard of care in neighbouring countries. While awareness of South–South medical travels has increased, only a few studies investigated this phenomenon in depth from the perspective of sending countries. This article aims to contribute to these studies by reporting findings from a qualitative study of medical travels from Cambodia and associated costs. Data collection primarily involved interviews with Cambodian patients returning from Thailand and Vietnam, conducted in 2017 in the capital Phnom Penh and two provinces, and interviews with key informants in the local health sector. The research findings show that medical travels from Cambodia are driven and shaped by an interplay of socio-economic, cultural and health system factors at different levels, from the effects of regional trade liberalization to perceptions about the quality of care and the pressure of relatives and other advisers in local communities. Furthermore, there is a diversity of medical travels from Cambodia, ranging from first class travels to international hospitals in Bangkok and cross-border ‘medical tourism’ to perilous overland journeys of poor patients, who regularly resort to borrowing or liquidating assets to cover costs. The implications of the research findings for health sector development and equitable access to care for Cambodians deserve particular attention. To some extent, the increase in medical travels can stimulate improvements in the quality of local health services. However, concerns remain that these developments will mainly affect high-cost private services, widening disparities in access to care between population groups.
Respiratory Tract Manifestations of Inflammatory Bowel Disease
Authors: Kröner Paul T , Lee Augustine , Farraye Francis A
Published: May 2020

Inflammatory bowel disease can manifest in many extraintestinal organ systems. The most frequently involved extraintestinal locations include the mucocutaneous, hepatobiliary, and ocular organ systems. The respiratory tract is less commonly involved and is therefore frequently overlooked. Consequently, it is believed that involvement of the respiratory tract in patients with inflammatory bowel disease is underreported. The pathogenesis is thought to be multifactorial, involving the common embryologic origin shared by the respiratory and luminal digestive tract, molecular mimicry, and immunologic interactions leading to immune-complex deposition in affected tissue. The spectrum of manifestations of the respiratory tract related to inflammatory bowel disease is broad. It not only includes direct involvement of the respiratory tract (ie, airways, interstitium, and pleura) but also can result as a consequence of systemic involvement such as in thromboembolic events. In addition, it may also be related to other conditions that affect the respiratory tract such as sarcoidosis and alpha-1 antitrypsin deficiency. Though some conditions related to respiratory tract involvement might be subclinical, others may have life-threatening consequences. It is critical to approach patients with suspected inflammatory bowel disease–related respiratory tract involvement in concert with pulmonology, infectious diseases, and any other pertinent experts, as treatments may require a multidisciplinary overlap of measures. Therefore, it is of paramount importance for the clinician to be aware of the array of respiratory tract manifestations of patients with inflammatory bowel disease, in addition to the possible spectrum of therapeutic measures.
Complete Kähler–Einstein Metric on Stein Manifolds With Negative Curvature
Authors: Lee Man-Chun
Published: May 2020

We show the existence of complete negative Kähler–Einstein metric on Stein manifolds with holomorphic sectional curvature bounded from above by a negative constant. We prove that any Kähler metrics on such manifolds can be deformed to the complete negative Kähler–Einstein metric using the normalized Kähler–Ricci flow.