bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and related Amaranthaceae: recombination and re-shuffling lead to a high structural variability
Authors: Maiwald Sophie , Weber Beatrice , Seibt Kathrin M , Schmidt Thomas , Heitkam Tony 
Published: September 2020

AbstractBackground and AimsPlant genomes contain many retrotransposons and their derivatives, which are subject to rapid sequence turnover. As non-autonomous retrotransposons do not encode any proteins, they experience reduced selective constraints leading to their diversification into multiple families, usually limited to a few closely related species. In contrast, the non-coding Cassandra terminal repeat retrotransposons in miniature (TRIMs) are widespread in many plants. Their hallmark is a conserved 5S rDNA-derived promoter in their long terminal repeats (LTRs). As sugar beet (Beta vulgaris) has a well-described LTR retrotransposon landscape, we aim to characterize TRIMs in beet and related genomes.MethodsWe identified Cassandra retrotransposons in the sugar beet reference genome and characterized their structural relationships. Genomic organization, chromosomal localization, and distribution of Cassandra-TRIMs across the Amaranthaceae were verified by Southern and fluorescent in situ hybridization.Key resultsAll 638 Cassandra sequences in the sugar beet genome contain conserved LTRs and thus constitute a single family. Nevertheless, variable internal regions required a subdivision into two Cassandra subfamilies within B. vulgaris. The related Chenopodium quinoa harbours a third subfamily. These subfamilies vary in their distribution within Amaranthaceae genomes, their insertion times and the degree of silencing by small RNAs. Cassandra retrotransposons gave rise to many structural variants, such as solo LTRs or tandemly arranged Cassandra retrotransposons. These Cassandra derivatives point to an interplay of template switch and recombination processes – mechanisms that likely caused Cassandra’s subfamily formation and diversification.ConclusionsWe traced the evolution of Cassandra in the Amaranthaceae and detected a considerable variability within the short internal regions, whereas the LTRs are strongly conserved in sequence and length. Presumably these hallmarks make Cassandra a prime target for unequal recombination, resulting in the observed structural diversity, an example of the impact of LTR-mediated evolutionary mechanisms on the host genome.
Tracking sickness effects on social encounters via continuous proximity sensing in wild vampire bats
Authors: Ripperger Simon P , Stockmaier Sebastian , Carter Gerald G 
Published: September 2020

Abstract
Sickness behaviors can slow the spread of pathogens across a social network. We conducted a field experiment to investigate how sickness behavior affects individual connectedness over time using a dynamic social network created from high-resolution proximity data. After capturing adult female vampire bats (Desmodus rotundus) from a roost, we created “sick” bats by injecting a random half of bats with the immune-challenging substance, lipopolysaccharide, while the control group received saline injections. Over the next 3 days, we used proximity sensors to continuously track dyadic associations between 16 “sick” bats and 15 control bats under natural conditions. Compared to control bats, “sick” bats associated with fewer bats, spent less time near others, and were less socially connected to more well-connected individuals (sick bats had on average a lower degree, strength, and eigenvector centrality). High-resolution proximity data allow researchers to flexibly define network connections (association rates) based on how a particular pathogen is transmitted (e.g., contact duration of &gt;1 vs. &gt;60 min, contact proximity of &lt;1 vs. &lt;10 m). Therefore, we inspected how different ways of measuring association rates changed the observed effect of LPS. How researchers define association rates influences the magnitude and detectability of sickness effects on network centrality. When animals are sick, they often encounter fewer individuals. We tracked this unintentional “social distancing” effect hour-by-hour in a wild colony of vampire bats. Using bat-borne proximity sensors, we compared changes in the social network connectedness of immune-challenged “sick” bats versus “control” bats over time. “Sick” bats had fewer encounters with others and spent less time near others. Associations changed dramatically by time of day, and different measures of association influenced the sickness effect estimates.
Predicting candidate genes from phenotypes, functions and anatomical site of expression
Authors: Chen Jun , Althagafi Azza , Hoehndorf Robert 
Published: September 2020

Abstract

Motivation
Over the past years, many computational methods have been developed to incorporate information about phenotypes for disease–gene prioritization task. These methods generally compute the similarity between a patient’s phenotypes and a database of gene-phenotype to find the most phenotypically similar match. The main limitation in these methods is their reliance on knowledge about phenotypes associated with particular genes, which is not complete in humans as well as in many model organisms, such as the mouse and fish. Information about functions of gene products and anatomical site of gene expression is available for more genes and can also be related to phenotypes through ontologies and machine-learning models.

Results
We developed a novel graph-based machine-learning method for biomedical ontologies, which is able to exploit axioms in ontologies and other graph-structured data. Using our machine-learning method, we embed genes based on their associated phenotypes, functions of the gene products and anatomical location of gene expression. We then develop a machine-learning model to predict gene–disease associations based on the associations between genes and multiple biomedical ontologies, and this model significantly improves over state-of-the-art methods. Furthermore, we extend phenotype-based gene prioritization methods significantly to all genes, which are associated with phenotypes, functions or site of expression.

Availability and implementation
Software and data are available at https://github.com/bio-ontology-research-group/DL2Vec.

Supplementary information
Supplementary data are available at Bioinformatics online.
Social policy practice preferences by social work students: Implications for macro practice education
Authors: Pawar Manohar , Nixon Maxwell 
Published: September 2020

Abstract
This article aims to discuss social work students’ choices of issues/needs for social policy practice and how those choices of policy issues can be employed to refine social policy education and training so as to better engage social work students and practitioners in policy practice. By employing reflective and secondary data analysis methods, the article looks at social policy practice assessments of social work students and identifies the chosen social issues/needs for setting the agenda, advocacy and policy analysis. The analysis shows a wide range of social issues/needs chosen by students for policy practice, without any particular pattern, and offers insights on how to design student-centred learning for policy practice assessments. It argues for the expansion of the knowledge and skills-base of the social work profession to create a balance between micro and macro practice. The reflective discussion suggests the implications for innovative ways of designing curriculum for macro social work education and preparing students for policy practice.
Quantitative spinal cord MRI in MOG-antibody disease, neuromyelitis optica and multiple sclerosis
Authors: Mariano Romina , Messina Silvia , Roca-Fernandez Adriana , Leite Maria I , Kong Yazhuo , Palace Jacqueline A 
Published: September 2020

Abstract
Spinal cord involvement is a hallmark feature of multiple sclerosis, neuromyelitis optica with AQP4 antibodies and MOG-antibody disease. In this cross-sectional study we use quantitative spinal cord MRI to better understand these conditions, differentiate them and associate with relevant clinical outcomes. Eighty participants (20 in each disease group and 20 matched healthy volunteers) underwent spinal cord MRI (cervical cord: 3D T1, 3D T2, diffusion tensor imaging and magnetization transfer ratio; thoracic cord: 3D T2), together with disability, pain and fatigue scoring. All participants had documented spinal cord involvement and were at least 6 months post an acute event. MRI scans were analysed using publicly available software. Those with AQP4-antibody disease showed a significant reduction in cervical cord cross-sectional area (P = 0.038), thoracic cord cross-sectional area (P = 0.043), cervical cord grey matter (P = 0.011), magnetization transfer ratio (P ≤ 0.001), fractional anisotropy (P = 0.004) and increased mean diffusivity (P = 0.008). Those with multiple sclerosis showed significantly increased mean diffusivity (P = 0.001) and reduced fractional anisotropy (P = 0.013), grey matter volume (P = 0.002) and magnetization transfer ratio (P = 0.011). In AQP4-antibody disease the damage was localized to areas of the cord involved in the acute attack. In multiple sclerosis this relationship with lesions was absent. MOG-antibody disease did not show significant differences to healthy volunteers in any modality. However, when considering only areas involved at the time of the acute attack, a reduction in grey matter volume was found (P = 0.023). This suggests a predominant central grey matter component to MOG-antibody myelitis, which we hypothesize could be partially responsible for the significant residual sphincter dysfunction. Those with relapsing MOG-antibody disease showed a reduction in cord cross-sectional area compared to those with monophasic disease, even when relapses occurred elsewhere (P = 0.012). This suggests that relapsing MOG-antibody disease is a more severe phenotype. We then applied a principal component analysis, followed by an orthogonal partial least squares analysis. MOG-antibody disease was discriminated from both AQP4-antibody disease and multiple sclerosis with moderate predictive values. Finally, we assessed the clinical relevance of these metrics using a multiple regression model. Cervical cord cross-sectional area associated with disability scores (B = −0.07, P = 0.0440, R2 = 0.20) and cervical cord spinothalamic tract fractional anisotropy associated with pain scores (B = −19.57, P = 0.016, R2 = 0.55). No spinal cord metric captured fatigue. This work contributes to our understanding of myelitis in these conditions and highlights the clinical relevance of quantitative spinal cord MRI.
The association between systemic autoimmune disorders and epilepsy and its clinical implications
Authors: Steriade Claude , Titulaer Maarten J , Vezzani Annamaria , Sander Josemir W , Thijs Roland D 
Published: September 2020

AbstractSystemic autoimmune disorders occur more frequently in patients with epilepsy than in the general population, suggesting shared disease mechanisms. The risk of epilepsy is elevated across the spectrum of systemic autoimmune disorders but is highest in systemic lupus erythematosus and type 1 diabetes mellitus. Vascular and metabolic factors are the most important mediators between systemic autoimmune disorders and epilepsy. Systemic immune dysfunction can also affect neuronal excitability, not only through innate immune activation and blood–brain barrier dysfunction in most epilepsies but also adaptive immunity in autoimmune encephalitis. The presence of systemic autoimmune disorders in subjects with acute seizures warrants evaluation for infectious, vascular, toxic and metabolic causes of acute symptomatic seizures, but clinical signs of autoimmune encephalitis should not be missed. Immunosuppressive medications may have antiseizure properties and trigger certain drug interactions with antiseizure treatments. A better understanding of mechanisms underlying the co-existence of epilepsy and systemic autoimmune disorders is needed to guide new antiseizure and anti-epileptogenic treatments. This review aims to summarize the epidemiological evidence for systemic autoimmune disorders as comorbidities of epilepsy, explore potential immune and non-immune mechanisms, and provide practical implications on diagnostic and therapeutic approach to epilepsy in those with comorbid systemic autoimmune disorders.
Nationwide Trends of Invasive Pneumococcal Disease in Spain From 2009 Through 2019 in Children and Adults During the Pneumococcal Conjugate Vaccine Era
Authors: de Miguel Sara , Domenech Mirian , González-Camacho Fernando , Sempere Julio , Vicioso Dolores , Sanz Juan Carlos , Comas Luis García , Ardanuy Carmen , Fenoll Asunción , Yuste Jose 
Published: September 2020

Abstract

Background
Introduction of pneumococcal conjugate vaccines (PCVs) has reduced the disease caused by vaccine serotypes in children, providing herd protection to adults. However, the emergence of nonvaccine serotypes is of great concern worldwide.

Methods
This study includes national laboratory data from invasive pneumococcal disease (IPD) cases that affected pediatric and adult populations during 2009–2019. The impact of implementing different vaccine strategies for immunocompetent adults by comparing Spanish regions that used the 13-valent PCV (PCV13) vs regions that used the 23-valent pneumococcal polysaccharide vaccine (PPV23) was also analyzed for 2017−2019.

Results
The overall reductions in IPD cases by PCV13 serotypes in children and adults were 88% and 59%, respectively, during 2009–2019, with a constant increase in serotype 8 in adults since 2015. IPD cases by additional serotypes covered by PPV23 increased from 20% in 2009 to 52% in 2019. In children, serotype 24F was the most frequent in 2019, whereas serotypes 3 and 8 accounted for 36% of IPD cases in adults. Introduction of PCV13 or PPV23 in the adult calendar of certain Spanish regions reduced the IPD cases by PCV13 serotypes by up to 25% and 11%, respectively, showing a decrease of serotype 3 when PCV13 was used.

Conclusions
Use of PCV13 in children has affected the epidemiology, reducing the burden of IPD in children but also in adults by herd protection; however, the increase in serotype 8 in adults is worrisome. Vaccination with PCV13 in adults seems to control IPD cases by PCV13 serotypes including serotype 3.
Brexit Uncertainty and Trade Disintegration
Authors: Graziano Alejandro G , Handley Kyle , Limão Nuno 
Published: September 2020

Abstract
We estimate the uncertainty effects of preferential trade disagreements. Increases in the probability of Britain’s exit from the European Union (Brexit) reduce bilateral export values and trade participation. These effects are increasing in trade policy risk across products. We estimate that at the average disagreement tariff of 4.5% the increase in the probability of Brexit after the referendum lowered EU–UK bilateral export values between 11–20%. Neither the EU or UK exporters believed a trade war was likely.
Factors affecting health promoting behavior among older women in Korea: a structural equation model
Authors: Oh Jihyun 
Published: September 2020

SummaryThe purpose of this study was to explain the health promoting behaviors of older women in South Korea using a structural equation model. The health promotion model developed by Pender was used. A survey using self-administered questionnaires was carried out between 2 October 2016 and 26 November 2016, with 252 older women ≥65 years living in Korea. The data were analyzed using structural equation modeling. The fitness parameters of the modified model (χ2 = 227.243, df = 176, χ2/df = 1.29, p = 0.006, root mean square error of approximation = 0.034, goodness of fit index = 0.927, Tucker−Lewis Index = 0.979, comparative fit index = 0.984, normed fit index = 0.933) indicated its suitability as the research model. Perceived benefits of action and social support directly influenced health promoting behavior, and prior related behavior indirectly influenced health promoting behavior. Interventions should aim to directly improve social support and perceived benefits to increase health promoting behaviors.
Kisspeptin deficiency leads to abnormal adrenal glands and excess steroid hormone secretion
Authors: Berthon Annabel , Settas Nikolaos , Delaney Angela , Giannakou Andreas , Demidowich Andrew , Faucz Fabio R , Seminara Stephanie B , Chen Margaret E , Stratakis Constantine A 
Published: September 2020

Abstract
Knockout mice for the kisspeptin receptor, Kiss1r (Kiss1r−/−) and its ligand kisspeptin, Kiss1 (Kiss1−/−) replicate the phenotype of isolated hypogonadotropic hypogonadism (IHH) associated with variants of these genes in humans. A recent report suggests that kisspeptin may be involved in human fetal adrenocortical development and function. Herein, we characterized the adrenal function and morphology in Kiss1−/− mice that do not go through normal puberty. Two fetal markers were expressed in eosinophilic cells potentially derived from the X-zone that should disappear at puberty in male mice and during the first pregnancy in female animals. Although the hypercorticosteronism observed in Kiss1−/− females corrected overtime, hyperaldosteronism persisted at 14 months and correlated with the overexpression of Star. To determine if KISS1 and KISS1R genes are involved in the development of primary aldosteronism (PA) and hypercortisolism [Cushing’s syndrome (CS)] in humans, we sequenced these 2 genes in 65 patients with PA and/or CS. Interestingly, a patient with CS presented with a germline KISS1 variant (p.H90D, rs201073751). We also found three rare variants in the KISS1R gene in three patients with PA: p.C95W (rs141767649), p.A189T (rs73507527) and p.R229R (rs115335009). The two missense variants have been previously associated with IHH. Our findings suggest that KISS1 may play a role in adrenal function in mice and possibly adrenocortical steroid hormone secretion in humans, beyond its recently described role in human fetal adrenocortical development.
Dystroglycan regulates proper expression, submembranous localization and subsequent phosphorylation of Dp71 through physical interaction
Authors: Fujimoto Takahiro , Yaoi Takeshi , Tanaka Hidekazu , Itoh Kyoko 
Published: September 2020

Abstract
Dystrophin–dystroglycan complex (DGC) plays important roles for structural integrity and cell signaling, and its defects cause progressive muscular degeneration and intellectual disability. Dystrophin short product, Dp71, is abundantly expressed in multiple tissues other than muscle and is suspected of contributing to cognitive functions; however, its molecular characteristics and relation to dystroglycan (DG) remain unknown. Here, we report that DG physically interacts with Dp71 in cultured cells. Intriguingly, DG expression positively and DG knockdown negatively affected the steady-state expression, submembranous localization and subsequent phosphorylation of Dp71. Mechanistically, two EF-hand regions along with a ZZ motif of Dp71 mediate its association with the transmembrane proximal region, amino acid residues 788–806, of DG cytoplasmic domain. Most importantly, the pathogenic point mutations of Dp71, C272Y in the ZZ motif or L170del in the second EF-hand region, impaired its binding to DG, submembranous localization and phosphorylation of Dp71, indicating the relevance of DG-dependent Dp71 regulatory mechanism to pathophysiological conditions. Since Dp140, another dystrophin product, was also regulated by DG in the same manner as Dp71, our results uncovered a tight molecular relation between DG and dystrophin, which has broad implications for understanding the DGC-related cellular physiology and pathophysiology.
Evaluation of extended thymectomy approaches based on residual fat tissue
Authors: Yoshida Mitsuteru , Yuasa Masao , Kondo Kazuya , Tsuboi Mitsuhiro , Kawakita Naoya , Tangoku Akira 
Published: September 2020

Abstract

OBJECTIVES
This study analysed the patterns of extraction ranges, characteristics, advantages and disadvantages of median sternotomy (MS) and subxiphoid (SX) approaches for extended thymectomy.

METHODS
This study included patients with anterior mediastinum tumour and myasthenia gravis who underwent extended thymectomy at our institution between 2015 and 2018. There were 5 MS and 6 SX extended thymectomy surgeries with the VINCENT software. On preoperative computed tomography, the thymus area and fat tissue surrounding the thymus, which were planned for extraction, were traced using VINCENT (Ver. 4.0). We then constructed three-dimensional images and calculated the volumes. Evaluation of the extended thymectomy approach based on the residual fat tissue was required to determine the area of extended thymectomy.

RESULTS
No significant differences in operation time (min) [SX: 197.3 ± 34.0, MS: 206.6 ± 91.4, drainage duration (days), SX: 2.2 ± 1.0, MS: 2.2 ± 0.4, hospital stay (days), SX: 11.8 ± 1.2, MS: 13.4 ± 2.1, residual rate (%), SX: 29.9 ± 17.5, MS: 58.7 ± 18.0 (P = 0.0519)] were observed between the 2 groups. Bleeding was significantly lower for SX than for MS. The residual rate was lower for SX than for MS.

CONCLUSIONS
Considering the amount of the residual fat tissue, the SX approach allows an adequate dissection area for extended thymectomy compared with the MS approach.
Rotavirus Genotypes in Hospitalized Children With Acute Gastroenteritis Before and After Rotavirus Vaccine Introduction in Blantyre, Malawi, 1997–2019
Authors: Mhango Chimwemwe , Mandolo Jonathan J , Chinyama End , Wachepa Richard , Kanjerwa Oscar , Malamba-Banda Chikondi , Matambo Prisca B , Barnes Kayla G , Chaguza Chrispin , Shawa Isaac T , Nyaga Martin M , Hungerford Daniel , Parashar Umesh D , Pitzer Virginia E , Kamng’ona Arox W , Iturriza-Gomara Miren , Cunliffe Nigel A , Jere Khuzwayo C 
Published: September 2020

Abstract

Background
Rotavirus vaccine (Rotarix [RV1]) has reduced diarrhea-associated hospitalizations and deaths in Malawi. We examined the trends in circulating rotavirus genotypes in Malawi over a 22-year period to assess the impact of RV1 introduction on strain distribution.

Methods
Data on rotavirus-positive stool specimens among children aged &lt;5 years hospitalized with diarrhea in Blantyre, Malawi before (July 1997–October 2012, n = 1765) and after (November 2012–October 2019, n = 934) RV1 introduction were analyzed. Rotavirus G and P genotypes were assigned using reverse-transcription polymerase chain reaction.

Results
A rich rotavirus strain diversity circulated throughout the 22-year period; Shannon (H′) and Simpson diversity (D′) indices did not differ between the pre- and postvaccine periods (H′ P &lt; .149; D′ P &lt; .287). Overall, G1 (n = 268/924 [28.7%]), G2 (n = 308/924 [33.0%]), G3 (n = 72/924 [7.7%]), and G12 (n = 109/924 [11.8%]) were the most prevalent genotypes identified following RV1 introduction. The prevalence of G1P[8] and G2P[4] genotypes declined each successive year following RV1 introduction, and were not detected after 2018. Genotype G3 reemerged and became the predominant genotype from 2017 onward. No evidence of genotype selection was observed 7 years post–RV1 introduction.

Conclusions
Rotavirus strain diversity and genotype variation in Malawi are likely driven by natural mechanisms rather than vaccine pressure.