bluuebunny/crossref_metadata_2025_split huggingface dataset:
NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks
Authors: Huang Neng , Nie Fan , Ni Peng , Luo Feng , Gao Xin , Wang Jianxin 
Published: May 2021

Abstract

Motivation
Oxford Nanopore sequencing producing long reads at low cost has made many breakthroughs in genomics studies. However, the large number of errors in Nanopore genome assembly affect the accuracy of genome analysis. Polishing is a procedure to correct the errors in genome assembly and can improve the reliability of the downstream analysis. However, the performances of the existing polishing methods are still not satisfactory.

Results
We developed a novel polishing method, NeuralPolish, to correct the errors in assemblies based on alignment matrix construction and orthogonal Bi-GRU networks. In this method, we designed an alignment feature matrix for representing read-to-assembly alignment. Each row of the matrix represents a read, and each column represents the aligned bases at each position of the contig. In the network architecture, a bi-directional GRU network is used to extract the sequence information inside each read by processing the alignment matrix row by row. After that, the feature matrix is processed by another bi-directional GRU network column by column to calculate the probability distribution. Finally, a CTC decoder generates a polished sequence with a greedy algorithm. We used five real datasets and three assembly tools including Wtdbg2, Flye and Canu for testing, and compared the results of different polishing methods including NeuralPolish, Racon, MarginPolish, HELEN and Medaka. Comprehensive experiments demonstrate that NeuralPolish achieves more accurate assembly with fewer errors than other polishing methods and can improve the accuracy of assembly obtained by different assemblers.

Availability and implementation
https://github.com/huangnengCSU/NeuralPolish.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
Impact of Stress on Job Engagement among Social Workers in Beijing: The Roles of Positive Emotion and Career Resilience
Authors: Zhang Huiping , Zhu Xuanbai , Yu Xiaowen 
Published: May 2021

Abstract
In China, social workers face great at-work stress, job burnout and turnover. Determining how to prevent and alleviate their job burnout and improve their work enthusiasm and engagement has become urgent. Using the affective events theory and challenge stressor-hindrance stressor framework, this study explored the impacts of different types of stressors on job engagement and its associated mechanisms and then examined the protective roles of positive emotion and career resilience. A total of 430 social workers in Beijing were investigated. The unique and combined contribution of the stress components to job engagement has been examined. The results showed that both challenge stressors and hindrance stressors had significantly negative impacts on social workers’ work engagement and positive emotion, and positive emotion had a significant positive influence on work engagement. Positive emotion fully mediated the negative relationship between challenge stressors and work engagement, and partially mediated the negative relationship between hindrance stressors and work engagement. Furthermore, career resilience can buffer the negative influence of challenge stressors on positive emotion.
Disaster Preparedness in Social Work: A Scoping Review of Evidence for Further Research, Theory and Practice
Authors: Boetto Heather , Bell Karen , Ivory Nicola 
Published: May 2021

AbstractThe aim of this study was to understand the extent and nature of social work literature relating to preparedness in the context of natural disasters and to identify the implications for further research, theory and practice. A systematic scoping review explored scholarly databases pertaining to literature about social work and disaster preparedness, between 2000 and 2019; a total of thirty-nine articles met the inclusion criteria. Data were extracted from these articles to map the range and type of literature, and thematic analysis was undertaken to explore aspects of preparedness in greater depth. Analysis revealed a recurring theme regarding the need to foreground preparedness in social work and disaster practice along with recommendations that preparedness be more consistently enacted as an ongoing, localised, dynamic and dialogic process in order to better respond to a diverse range of community needs. Building on these findings, the authors highlight the need to challenge dominant discourses in social work and extend the conceptualisation of the profession in the context of disasters at both the intra- and inter-professional levels. By drawing on transformative, ecosocial approaches, the profession’s contributions to disaster practice, equity and justice in this complex context of global practice can gain visibility.
Biallelic mutations in RNF220 cause laminopathies featuring leukodystrophy, ataxia and deafness
Authors: Sferra Antonella , Fortugno Paola , Motta Marialetizia , Aiello Chiara , Petrini Stefania , Ciolfi Andrea , Cipressa Francesca , Moroni Isabella , Leuzzi Vincenzo , Pieroni Luisa , Marini Federica , Boespflug Tanguy Odile , Eymard-Pierre Eleonore , Danti Federica Rachele , Compagnucci Claudia , Zambruno Giovanna , Brusco Alfredo , Santorelli Filippo M , Chiapparini Luisa , Francalanci Paola , Loizzo Anna Livia , Tartaglia Marco , Cestra Gianluca , Bertini Enrico 
Published: May 2021

Abstract
Leukodystrophies are a heterogeneous group of rare inherited disorders that mostly involve the white matter of the CNS. These conditions are characterized by primary glial cell and myelin sheath pathology of variable aetiology, which causes secondary axonal degeneration, generally emerging with disease progression.
Whole exome sequencing performed in five large consanguineous nuclear families allowed us to identify homozygosity for two recurrent missense variants affecting highly conserved residues of RNF220 as the causative event underlying a novel form of leukodystrophy with ataxia and sensorineural deafness.
We report these two homozygous missense variants (p.R363Q and p.R365Q) in the ubiquitin E3 ligase RNF220 as the underlying cause of this novel form of leukodystrophy with ataxia and sensorineural deafness that includes fibrotic cardiomyopathy and hepatopathy as associated features in seven consanguineous families. Mass spectrometry analysis identified lamin B1 as the RNF220 binding protein and co-immunoprecipitation experiments demonstrated reduced binding of both RNF220 mutants to lamin B1. We demonstrate that RNF220 silencing in Drosophila melanogaster specifically affects proper localization of lamin Dm0, the fly lamin B1 orthologue, promotes its aggregation and causes a neurodegenerative phenotype, strongly supporting the functional link between RNF220 and lamin B1. Finally, we demonstrate that RNF220 plays a crucial role in the maintenance of nuclear morphology; mutations in primary skin fibroblasts determine nuclear abnormalities such as blebs, herniations and invaginations, which are typically observed in cells of patients affected by laminopathies.
Overall, our data identify RNF220 as a gene implicated in leukodystrophy with ataxia and sensorineural deafness and document a critical role of RNF220 in the regulation of nuclear lamina. Our findings provide further evidence on the direct link between nuclear lamina dysfunction and neurodegeneration.
Molecular Epidemiology, Natural History, and Long-Term Outcomes of Multidrug-Resistant Enterobacterales Colonization and Infections Among Solid Organ Transplant Recipients
Authors: Hong Nguyen M , Shields Ryan K , Chen Liang , William Pasculle A , Hao Binghua , Cheng Shaoji , Sun Jonathan , Kline Ellen G , Kreiswirth Barry N , Clancy Cornelius J 
Published: May 2021

Abstract

Background
Multidrug-resistant Enterobacterales (MDR-E), including carbapenem-resistant and third-generation cephalosporin-resistant Enterobacterales (CRE, CefR-E), are major pathogens following solid organ transplantation (SOT).

Methods
We prospectively studied patients who underwent lung, liver, and small bowel transplant from February 2015 through March 2017. Weekly perirectal swabs (up to 100 days post-transplant) were cultured for MDR-E. Whole-genome sequencing (WGS) was performed on gastrointestinal (GI) tract–colonizing and disease-causing isolates.

Results
Twenty-five percent (40 of 162) of patients were MDR-E GI-colonized. Klebsiella pneumoniae was the most common CRE and CefR-E. Klebsiella pneumoniae carbapenemases and CTX-M were leading causes of CR and CefR, respectively. Thirty-five percent of GI colonizers developed MDR-E infection vs 2% of noncolonizers (P &lt; .0001). The attack rate was higher among CRE colonizers than CefR-E colonizers (53% vs 21%, P = .049). GI colonization and high body mass index were independent risk factors for MDR-E infection (P ≤ .004). Thirty-day mortality among infected patients was 6%. However, 44% of survivors developed recurrent infections; 43% of recurrences were late (285 days to 3.9 years after the initial infection). Long-term survival (median, 4.3 years post-transplant) did not differ significantly between MDR-E–infected and MDR-E–noninfected patients (71% vs 77%, P = .56). WGS phylogenetic analyses revealed that infections were caused by GI-colonizing strains and suggested unrecognized transmission of novel clonal group-258 sublineage CR-K. pneumoniae and horizontal transfer of resistance genes.

Conclusions
MDR-E GI colonization was common following SOT and predisposed patients to infections by colonizing strains. MDR-E infections were associated with low short- and long-term mortality, but recurrences were frequent and often occurred years after initial infections. Findings provide support for MDR-E surveillance in our SOT program.
Arginase II protein regulates Parkin-dependent p32 degradation that contributes to Ca2+-dependent eNOS activation in endothelial cells
Authors: Koo Bon-Hyeock , Won Moo-Ho , Kim Young-Myeong , Ryoo Sungwoo 
Published: May 2021

Abstract

Aims
Arginase II (ArgII) plays a key role in the regulation of Ca2+ between the cytosol and mitochondria in a p32-dependent manner. p32 contributes to endothelial nitric oxide synthase (eNOS) activation through the Ca2+/CaMKII/AMPK/p38MAPK/Akt signalling cascade. Therefore, we investigated a novel function of ArgII in the regulation of p32 stability.

Methods and results
mRNA levels were measured by quantitative reverse transcription-PCR, and protein levels and activation were confirmed by western blot analysis. Ca2+ concentrations were measured by FACS analysis and a vascular tension assay was performed. ArgII bound to p32, and ArgII protein knockdown using siArgII facilitated the ubiquitin-dependent proteasomal degradation of p32. β-lactone, a proteasome inhibitor, inhibited the p32 degradation associated with endothelial dysfunction in a Ca2+-dependent manner. The amino acids Lys154, Lys 180, and Lys220 of the p32 protein were identified as putative ubiquitination sites. When these sites were mutated, p32 was resistant to degradation in the presence of siArgII, and endothelial function was impaired. Knockdown of Pink/Parkin as an E3-ubiquitin ligase with siRNAs resulted in increased p32, decreased [Ca2+]c, and attenuated CaMKII-dependent eNOS activation by siArgII. siArgII-dependent Parkin activation was attenuated by KN93, a CaMKII inhibitor. Knockdown of ArgII mRNA and its gene, but not inhibition of its activity, accelerated the interaction between p32 and Parkin and reduced p32 levels. In aortas of ArgII−/− mice, p32 levels were reduced by activated Parkin and inhibition of CaMKII attenuated Parkin-dependent p32 lysis. siParkin blunted the phosphorylation of the activated CaMKII/AMPK/p38MAPK/Akt/eNOS signalling cascade. However, ApoE−/− mice fed a high-cholesterol diet had greater ArgII activity, significantly attenuated phosphorylation of Parkin, and increased p32 levels. Incubation with siArgII augmented p32 ubiquitination through Parkin activation, and induced signalling cascade activation.

Conclusion
The results suggest a novel function for ArgII protein in Parkin-dependent ubiquitination of p32 that is associated with Ca2+-mediated eNOS activation in endothelial cells.
MTDH Promotes Intestinal Inflammation by Positively Regulating TLR Signalling
Authors: Wang Lijuan , Zhang Ning , Han Dianwen , Su Peng , Chen Bing , Zhao Wenjing , Liu Ying , Zhang Hanwen , Hu Guohong , Yang Qifeng 
Published: May 2021

Abstract
Macrophages in the intestinal mucosa can rapidly engage Toll-like receptor [TLR]-mediated inflammatory responses to protect against pathogen invasion, but these same innate immune responses can also drive the induction of colitis. Our previous research revealed that metadherin [MTDH] is overexpressed in multiple cancers and plays vital roles in tumour progression. However, the role of MTDH in intestinal inflammation is largely unknown. In this study, we found the MTDH expression in colonic lamina propria [CLP] macrophages was positively correlated with inflammatory colitis severity. MTDH-/- mice were protected against the symptoms of dextran sodium sulphate [DSS]-induced colitis; however, adoptive transfer of MTDH wild-type [WT] monocytes partially restored the susceptibility of MTDH-/- mice to DSS-induced colitis. TLR stimulation was sufficient to induce the expression of MTDH, whereas the absence of MTDH was sufficient to suppress TLR-induced production of inflammatory cytokines by macrophages. From a mechanistic perspective, MTDH recruited TRAF6 to TAK1, leading to TRAF6-mediated TAK1 K63 ubiquitination and phosphorylation, ultimately facilitating TLR-induced NF-κB and MAPK signalling. Taken together, our results indicate that MTDH contributes to colitis development by promoting TLR-induced pro-inflammatory cytokine production in CLP macrophages and might represent a potential therapeutic approach for intestine inflammation intervention.
Chicago Bees: Urban Areas Support Diverse Bee Communities but With More Non-Native Bee Species Compared to Suburban Areas
Authors: Gruver Andrea , CaraDonna Paul 
Published: May 2021

AbstractUrbanization is rapidly growing worldwide, yet we still do not fully understand how it affects many organisms. This may be especially true for wild bees that require specific nesting and floral resources and have been threatened by habitat loss. Our study explores the response of wild bee communities to an urbanization gradient in the Chicagoland region of Illinois. Specifically, we explored how both landscape scale impervious surface and local floral diversity across an urbanization gradient influenced 1) the composition of local bee communities, 2) the richness of native and non-native bees, and 3) the composition of bee functional traits. Over the course of our study, we documented 2,331 bees belonging to 83 different species, 13 of which were not native to North America. We found that impervious surface influenced the overall composition of bee communities. In particular, highly urban areas were composed of more non-native bee species and fewer native bee species. Additionally, bee richness and native bee richness responded positively to floral resources. Bee functional trait responses were variable, with floral diverse sites supporting greater richness of ground nesting, eusocial, and generalist bees regardless of landscape-level impervious surface. Importantly, our study provides evidence that urban areas can support diverse bee communities, but urban and suburban bee communities do differ in composition. Thus, bee conservation efforts in urban areas should focus on creating floral diverse habitats to help support more bee species, specifically native bee species, while also considering which bees are best supported by these conservation efforts.
ST-segment elevation myocardial infarction with normal coronary arteries secondary to anterior communicating cerebral artery aneurysmal rupture: a case report
Authors: Lwin Tin Sanda , Mitrakrishnan Rayno Navinan , Farooq Mohisin , Alama Mohamed 
Published: May 2021

Abstract

Background
Myocardial infarction (MI) with non-obstructive coronary arteries presenting with ST-segment elevation can be challenging. Understanding the cardiac and non-cardiac causes aid in identifying the underlying diagnosis and deciding on the management. Neurological insult resulting in a mismatch of oxygen supply or demand to cardiomyocytes can lead to type 2 MI. Acute brain injury, such as intracranial haemorrhage, can induce cardiac dysfunction secondary to brain–heart interaction via hypothalamic–pituitary–adrenal axis and catecholamine surge.

Case summary
A 50-year-old Caucasian male who vaped cannabis presented with epileptic seizures. A Glasgow coma scale of 7/15 necessitated urgent intubation. Electrocardiogram showed ST-segment elevation in inferior leads. Computed tomography of the head suggested intracerebral haemorrhage. He was stabilized in the intensive care unit (ICU). Subsequent imaging confirmed anterior communicating cerebral artery aneurysm and haematoma. Echocardiogram showed severe left ventricular dysfunction and hypokinesia in the left circumflex (LCx) territory. After step down from ICU, cardiac magnetic resonance imaging revealed transmural MI and myocardial oedema at LCx territory. Coronary angiogram was normal. Patient was treated with Levetiracetam and heart failure regimen. A cardiac defibrillator was implanted for secondary prevention and he was scheduled for elective neurosurgical intervention. A follow-up outpatient echocardiogram was normal.

Discussion
Myocardial infarction with non-obstructive coronary arteries is uncommon. Though the majority is due to either plaque disruption or myocarditis, non-cardiac causes, such as acute neurological insults and substance use, should be considered. Scrutinizing the clinical presentation and using a meticulous approach with appropriate investigations are required to reach the correct diagnosis and appropriate management.
Right aortic arch forming a true vascular ring: a clinical review
Authors: Biermann Daniel , Holst Theresa , Hüners Ida , Rickers Carsten , Kehl Torben , Rüffer André , Sachweh Jörg S , Hazekamp Mark G 
Published: May 2021

Abstract

OBJECTIVES
This review aims at presenting and summarizing the current state of literature on the presentation and surgical management of a right-sided aortic arch with a left-sided ligamentum forming a complete vascular ring around the oesophagus and trachea.

METHODS
A systematic database search for appropriate literature was conducted on PubMed/MEDLINE. Articles were considered relevant when providing details on the presentation, diagnosis and surgical treatment of this specific congenital arch anomaly in human beings.

RESULTS
Affected patients present with respiratory and/or oesophageal difficulties due to tracheoesophageal compression. Conservative treatment might be reasonable in asymptomatic or mildly symptomatic cases; however, once moderate-to-severe symptoms develop, surgical intervention is definitely indicated. Surgery is commonly performed through a left thoracotomy or median sternotomy and includes the division of the left ductal ligamentum; if a Kommerell's diverticulum is present that is &gt;1.5 times the diameter of the subclavian artery, then concomitant resection of the large diverticulum and translocation of the aberrant left subclavian artery is also conducted. Postoperative morbidity and mortality are low and are rather related to concomitant intracardiac and extracardiac anomalies than to the procedure itself. In a majority of patients, full resolution of symptoms is seen within months to years from the surgery. Nevertheless, there is also a subset of patients who remain with some tracheobronchial narrowing, sometimes even requiring reintervention during follow-up due to persisting or recurring symptoms.

CONCLUSIONS
Overall, the surgical management of a right aortic arch forming a true vascular ring in infancy, childhood and adulthood seems relatively safe and effective in providing symptomatic relief despite some persistent tracheobronchial and/or oesophageal narrowing in some cases.
Intraoperative transit-time flow measurement and high-frequency ultrasound in coronary artery bypass grafting: impact in off versus on-pump, arterial versus venous grafting and cardiac territory grafted
Authors: Rosenfeld Ethan S , Trachiotis Gregory D , Napolitano Michael A , Sparks Andrew D , Wendt Daniel , Kieser Teresa M , Puskas John D , DiGiammarco Gabriele , Taggart David P 
Published: May 2021

Abstract

OBJECTIVES
Despite society guideline recommendations, intraoperative high-frequency ultrasound (HFUS) and transit-time flow measurement (TTFM) use in coronary artery bypass grafting (CABG) has not been widely adopted worldwide. This retrospective review of the REQUEST (REgistry for QUality assESsmenT with Ultrasound Imaging and TTFM in Cardiac Bypass Surgery) study assesses the impact of protocolled high-frequency ultrasound/TTFM use in specific technical circumstances of CABG.

METHODS
Three REQUEST study sub-analyses were examined: (i) For off-pump (OPCAB) versus on-pump (ONCAB) procedures: strategy changes from preoperative plans for the aorta, conduits, coronary targets and graft revisions; and for all REQUEST patients, revision rates in: (ii) arterial versus venous grafts; and (iii) grafts to different cardiac territories.

RESULTS
Four hundred and two (39.6%) of 1016 patients undergoing elective isolated CABG for multivessel disease underwent OPCAB procedures. Compared to ONCAB, OPCAB patients experienced more strategy changes regarding the aorta [14.7% vs 3.4%; odds ratios (OR) = 4.03; confidence interval (CI) = 2.32–7.20], less regarding conduits (0.2% vs 2.8%; OR = 0.09; CI = 0.01–0.56), with no differences in coronary target changes or graft revisions (4.1% vs 3.5%; OR = 1.19; CI = 0.78–1.81). In all REQUEST patients, revisions were more common for arterial versus venous grafts (4.7% vs 2.4%; OR = 2.05; CI = 1.29–3.37), and inferior versus anterior (5.1% vs 2.9%; OR = 1.77; CI = 1.08–2.89) and lateral (5.1% vs 2.8%; OR = 1.83; CI = 1.04–3.27) territory grafts.

CONCLUSIONS
High-frequency ultrasound/TTFM use differentially impacts strategy changes and graft revision rates in different technical circumstances of CABG. Notably, patients undergoing OPCAB experienced 4 times more changes related to the ascending aorta than ONCAB patients. These findings may indicate where intraoperative assessment is most usefully applied.

Clinical trial registration number
ClinicalTrials.gov: NCT02385344