bluuebunny/crossref_metadata_2025_split huggingface dataset:
CNSA: a data repository for archiving omics data
Authors: Guo Xueqin , Chen Fengzhen , Gao Fei , Li Ling , Liu Ke , You Lijin , Hua Cong , Yang Fan , Liu Wanliang , Peng Chunhua , Wang Lina , Yang Xiaoxia , Zhou Feiyu , Tong Jiawei , Cai Jia , Li Zhiyong , Wan Bo , Zhang Lei , Yang Tao , Zhang Minwen , Yang Linlin , Yang Yawen , Zeng Wenjun , Wang Bo , Wei Xiaofeng , Xu Xun 
Published: April 2020

AbstractWith the application and development of high-throughput sequencing technology in life and health sciences, massive multi-dimensional biological data brings the problem of efficient management and utilization. Database development and biocuration are the prerequisites for the reuse of these big data. Here, relying on China National GeneBank (CNGB), we present CNGB Sequence Archive (CNSA) for archiving omics data, including raw sequencing data and its analytical data and related metadata which are organized into six objects, namely Project, Sample, Experiment, Run, Assembly, and Variation at present. Moreover, CNSA has created the correlation model of living samples, sample information, and analytical data on some projects, so that all data can be traced throughout the life cycle from the living sample to the sample information to the analytical data. Complying with the data standards commonly used in the life sciences, CNSA is committed to building a comprehensive and curated data repository for the storage, management and sharing of omics data, improving the data standards, and providing free access to open data resources for worldwide scientific communities to support academic research and the bio-industry. Database URL:https://db.cngb.org/cnsa/
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement
Authors: Liang Zhenlan , Li Min , Zheng Ruiqing , Tian Yu , Yan Xuhua , Chen Jin , Wu Fang-Xiang , Wang Jianxin 
Published: April 2020

AbstractAccurate identification of cell types from single-cell RNA sequencing (scRNA-seq) data plays a critical role in a variety of scRNA-seq analysis studies. It corresponds to solving an unsupervised clustering problem, in which the similarity measurement between cells in a high dimensional space affects the result significantly. Although many approaches have been proposed recently, the accuracy of cell type identification still needs to be improved. In this study, we proposed a novel single-cell clustering framework based on similarity learning, called SSRE. In SSRE, we model the relationships between cells based on subspace assumption and generate a sparse representation of the cell-to-cell similarity, which retains the most similar neighbors for each cell. Besides, we adopt classical pairwise similarities incorporated with a gene selection and enhancement strategy to further improve the effectiveness of SSRE. For performance evaluation, we applied SSRE in clustering, visualization, and other exploratory data analysis processes on various scRNA-seq datasets. Experimental results show that SSRE achieves superior performance in most cases compared to several state-of-the-art methods.
A novel hypomorphic allele ofSpag17causes primary ciliary dyskinesia phenotypes in mice
Authors: Abdelhamed Zakia , Lukacs Marshall , Cindric Sandra , Omran Heymut , Stottmann Rolf W. 
Published: April 2020

AbstractPrimary ciliary dyskinesia (PCD) is a human condition of dysfunctional motile cilia characterized by recurrent lung infection, infertility, organ laterality defects, and partially penetrant hydrocephalus. We recovered a mouse mutant from a forward genetic screen that developed all the phenotypes of PCD. Whole exome sequencing identified thisprimary ciliary dyskinesia only (Pcdo)allele to be a nonsense mutation (c.5236A>T) in theSpag17coding sequence creating a premature stop codon at position 1746 (K1746*). ThePcdovariant abolished different isoforms of SPAG17 in thePcdomutant testis but not in the brain. Our data indicate differential requirements for SPAG17 in different motile cilia cell types. SPAG17 is required for proper development of the sperm flagellum, and is essential for either development or stability of the C1 microtubule structure within cilia, but not the brain ependymal cilia. We identified changes in ependymal cilia beating frequency but these did not apparently alter lateral ventricle cerebrospinal fluid (CSF) flow. Aqueductal (Aq) stenosis resulted in significantly slower and abnormally directed CSF flow and we suggest this is the root cause of the hydrocephalus. TheSpag17Pcdohomozygous mutant mice are generally viable to adulthood, but have a significantly shortened life span with chronic morbidity. Our data indicate that the c.5236A>TPcdovariant is a hypomorphic allele ofSpag17gene that causes phenotypes related to motile, but not primary, cilia.Spag17Pcdois a novel and useful model for elucidating the molecular mechanisms underlying development of PCD in the mouse.
An insula-driven network computes decision uncertainty and promotes abstinence in chronic cocaine users
Authors: Yu Ju-Chi , Fiore Vincenzo G. , Briggs Richard W. , Braud Jacquelyn , Rubia Katya , Adinoff Bryon , Gu Xiaosi 
Published: April 2020

AbstractThe anterior insular cortex (AIC) and its interconnected brain regions have been associated with both addiction and decision-making under uncertainty. However, the causal interactions in this uncertainty-encoding neurocircuitry and how these neural dynamics impact relapse remain elusive. Here, we used model-based fMRI to measure choice uncertainty in a motor decision task in 61 individuals with cocaine use disorder (CUD) and 25 healthy controls. CUD participants were assessed before discharge from a residential treatment program and followed for up to 24 weeks. We found that choice uncertainty was tracked by the AIC, dorsal anterior cingulate cortex (dACC), and ventral striatum (VS), across participants. Stronger activations in these regions measured pre-discharge predicted longer abstinence after discharge in individuals with CUD. Dynamic causal modelling revealed an AIC-to-dACC directed connectivity modulated by uncertainty in controls, but a dACC-to-AIC connectivity in CUD participants. This reversal was mostly driven by early-relapsers (<30 days). Furthermore, CUD individuals who displayed a stronger AIC-to-dACC excitatory connection during uncertainty encoding remained abstinent for longer periods. These findings reveal a critical role of an AIC-driven, uncertainty-encoding neurocircuitry in protecting against relapse and promoting abstinence.
Prediction of Motor Imagery Tasks from Multi-Channel EEG Data for Brain-Computer Interface Applications
Authors: Miah Md. Ochiuddin , Rahman Md. Mahfuzur , Muhammod Rafsanjani , Farid Dewan Md. 
Published: April 2020

AbstractThe classification ofmotorimageryelectroencephalogram (MI-EEG) is a pivotal part of the biosignal classification in thebrain-computerinterface (BCI) applications. Currently, this bio-engineering based technology is being employed by researchers in various fields to develop cutting edge applications. The classification of real-time MI-EEG signal is the core computing and challenging task in these applications. It is well-known that the existing classification methods are not so accurate due to the high dimensionality and dynamic behaviors of the real-time EEG data. To improve the classification performance of real-time BCI applications, this paper presents a clustering-based ensemble technique and a developed brain game that distinguishes different human thoughts. At first, we have gathered the brain signals, extracted and selected informative features from these signals to generate training and testing sets. After that, we have constructed several classifiers using Artificial Neural Network (ANN), Support Vector Machine (SVM), naïve Bayes, Decision Tree (DT), Random Forest, Bagging, AdaBoost and compared the performance of these existing approaches with suggested clustering-based ensemble technique. On average, the proposed ensemble technique improved the classification accuracy of roughly 5 to 15% compared to the existing methods. Finally, we have developed the targeted brain game employing our suggested ensemble technique. In this game, real-time EEG signal classification and prediction tabulation through animated ball are controlled via threads. By playing this game, users can control the movements of the balls via the brain signals of motor imagery movements without using any traditional input devices. All relevant codes are available via open repository at:https://github.com/mrzResearchArena/MI-EEG.
Investigating Deep Feedforward Neural Networks for Classification of Transposon-Derived piRNAs
Authors: da Costa Alisson Hayasi , dos Santos Renato Augusto C. , Cerri Ricardo 
Published: April 2020

AbstractPIWI-Interacting RNAs (piRNAs) form an important class of non-coding RNAs that play a key role in the genome integrity through the silencing of transposable elements. However, despite their importance and the large application of deep learning in computational biology for classification tasks, there are few studies of deep learning and neural networks for piRNAs prediction. Therefore, this paper presents an investigation on deep feedforward networks models for classification of transposon-derived piRNAs. We analyze and compare the results of the neural networks in different hyperparameters choices, such as number of layers, activation functions and optimizers, clarifying the advantages and disadvantages of each configuration. From this analysis, we propose a model for human piRNAs classification and compare our method with the state-of-the-art deep neural network for piRNA prediction in the literature and also traditional machine learning algorithms, such as Support Vector Machines and Random Forests, showing that our model has achieved a great performance with an F-measure value of 0.872, outperforming the state-of-the-art method in the literature.
CBRPP: a new RNA-centric method to study RNA-protein interactions
Authors: Li Yunfei , Liu Shengde , Cao Lili , Luo Yujie , Du Hongqiang , Li Siji , You Fuping 
Published: April 2020

AbstractRNA-protein interactions play essential roles in tuning gene expression at RNA level and modulating the function of proteins. Abnormal RNA-protein interactions lead to cell dysfunction and human diseases. Therefore, mapping networks of RNA-protein interactions is crucial for understanding cellular mechanism and pathogenesis of diseases. Different practical protein-centric methods for studying RNA-protein interactions has been reported, but few RNA-centric methods exist. Here, we developed CRISPR-based RNA proximity proteomics (CBRPP), a new RNA-centric method to identify proteins associated with the target RNA in native cellular context without cross-linking or RNA manipulation in vitro. CBRPP is based on a fusion of dCas13 and proximity-based labeling (PBL) enzyme. dCas13 can deliver PBL enzyme to the target RNA with high specificity, while PBL enzyme labels the surrounding proteins of the target RNA, which are then identified by mass spectrometry.
A causal model of the declaration intention of banks for suspected money-laundering transactions based on organizational commitment perspective
Authors: Chan Te-En , Chan Ya-Hui , Lin Shu-Ping 
Published: April 2020

PurposeAnti-money laundering has attracted much global attention, driving banks to invest in the establishment of suspicious transaction report mechanisms for the declaration of suspicious transactions. However, very few studies discuss how to influence bank employees to proactively declare suspicious transactions. Therefore, the purpose of this study is to, based on an organizational commitment perspective, establish a causal model that can assist banks to identify key factors affecting the intention to declare suspicious transactions.Design/methodology/approachThis study first summarized five factors – regulatory focus, organization climate, situational constraints, personality traits and role stress – and their composition constructs as the basis for measurements. An interview-based survey of nine Taiwanese banks was conducted. Then, this study adopted the decision-making trial and evaluation laboratory method to analyse the interplay between the five factors to identify the causal model and to explore the differences in the effects of the key factors, arising from the different organizational and job patterns, on the intention to declare suspicious transactions.FindingsThe results show that regulatory focus and organizational climate are the most important causal factors affecting employees’ intention to declare suspicious transactions, whereas role stress and personality traits are the most influenced effect factors. In addition, this study also confirmed that under different organizational and job patterns, the understanding of employees will change.Originality/valueThis paper provides insight into the interplay between the five factors based on an organizational commitment perspective. The findings can assist banks in managing and monitoring the implementation of the suspicious transaction report mechanism.
Femoral nerve blocks for the treatment of acute pre‐hospital pain: A systematic review with meta‐analysis
Authors: Raatiniemi Lasse , Magnusson Vidar , Hyldmo Per K. , Friesgaard Kristian D. , Kongstad Poul , Kurola Jouni , Larsen Robert , Rehn Marius , Rognås Leif , Sandberg Mårten , Vist Gunn E. 
Published: April 2020

BackgroundPain management is one of the most important interventions in the emergency medical services. The femoral nerve block (FNB) is, among other things, indicated for pre‐ and post‐operative pain management for patients with femoral fractures but its role in the pre‐hospital setting has not been determined. The aim of this review was to assess the effect and safety of the FNB in comparison to other forms of analgesia (or no treatment) for managing acute lower extremity pain in adult patients in the pre‐hospital setting.MethodsA systematic review (PROSPERO registration (CRD42018114399)) was conducted. The Cochrane and GRADE methods were used to assess outcomes. Two authors independently reviewed each study for eligibility, extracted the data and performed risk of bias assessments.ResultsFour studies with a total of 252 patients were included. Two RCTs (114 patients) showed that FNB may reduce pain more effectively than metamizole (mean difference 32 mm on a 100 mm VAS (95% CI 24 to 40)). One RCT (48 patients) compared the FNB with lidocaine and magnesium sulphate to FNB with lidocaine alone and was only included here for information regarding adverse effects. One case series included 90 patients. Few adverse events were reported in the included studies. The certainty of evidence was very low. We found no studies comparing FNB to inhaled analgesics, opioids or ketamine.ConclusionsEvidence regarding the effectiveness and adverse effects of pre‐hospital FNB is limited. Studies comparing pre‐hospital FNB to inhaled analgesics, opioids or ketamine are lacking.
Ultrasound‐guided transmuscular quadratus lumborum catheters for elective caesarean section: A protocol for a single‐centre, double‐blind randomised trial
Authors: Steingrímsdóttir Guðný E. , Hansen Christian K. , Børglum Jens 
Published: April 2020

BackgroundManagement of moderate‐to‐severe post‐operative pain after elective caesarean section (ECS) is internationally primarily based on either epidural catheters or opioids. However, both techniques are associated with some undesirable adverse events. Bilateral transmuscular quadratus lumborum (TQL) block has proven to reduce opioid consumption significantly in the first 24 post‐operative hours following ECS and prolong time to first opioid (TFO) (Hansen CKD, Steingrimsdottir M, Laier GE, et al. Reg Anesth Pain Med. 2019; 10.1136/rapm‐2019‐100540). We present a randomised controlled trial aiming to investigate whether continuous analgesia via bilateral TQL catheters can prolong TFO after ECS.MethodsThis study is a double‐blind, randomised, placebo‐controlled trial. Patients should be 18 years or older and scheduled for ECS under spinal anaesthesia to be included. Main exclusion criteria are inability to cooperate, excessive daily intake of opioids and difficult ultrasound visualisation of muscular and fascial structures. Participants are randomised to receive ultrasound‐guided injection of either 30 mL ropivacaine 0.2% bilaterally and an elastomeric pump containing 0.2% ropivacaine, or 30 mL saline bilaterally and an elastomeric pump containing saline, 2 hours after catheter placement. The primary endpoint is TFO. Secondary outcomes include pain intensity on a numeric rating scale (NRS), accumulated morphine consumption during 24 hours, displacement frequency of catheters and morphine‐related adverse events.Recruitment periodFour patients were included from September 2018 to November 2018. Inclusion was resumed in June 2019 and will continue until 24 patients with useful data have been included in the trial. Expected inclusion period is 10‐14 months.Trial registrationClinicalTrials.gov identifier: NCT03663478.EudraCT: 2017‐003625‐15.
Patient and clinician perspectives on a patient‐facing dashboard that visualizes patient reported outcomes in rheumatoid arthritis
Authors: Liu Lucy H. , Garrett Sarah B. , Li Jing , Ragouzeos Dana , Berrean Beth , Dohan Daniel , Katz Patricia P. , Barton Jennifer L. , Yazdany Jinoos , Schmajuk Gabriela 
Published: April 2020

AbstractBackgroundPoor patient‐clinician communication around patient‐reported outcomes (PROs) is a barrier to the effective management of rheumatoid arthritis (RA). We aimed to develop an RA ‘dashboard’ that could facilitate conversations about PROs and that would be acceptable to a wide range of patients, including English and Spanish speakers and patients with adequate or limited health literacy.MethodsA diverse group of RA patients along with clinicians from two academic rheumatology clinics joined separate focus groups. We solicited feedback and made iterative changes to mock‐ups of an RA dashboard that visualized PROs using a human‐centred design process. We used the thematic analysis method to identify and characterize themes from the focus groups and used these insights to refine the dashboard.ResultsWe conducted six focus groups involving 25 RA patients and three groups with 11 clinicians. Patients and clinicians agreed that the dashboard could enhance communication about PROs and RA disease activity and could promote patient self‐management. Patients varied in their (a) comprehension, (b) preferences for the display and features of the dashboard, and (c) desired uses for the dashboard. Clinicians expressed significant concerns about the logistics of using the dashboard in clinical practice.ConclusionUsing principles of human‐centred design, we created an RA dashboard that was well‐accepted among patients and clinicians. The ability to customize the data display is important for tailoring the dashboard to patients with diverse needs and preferences. Special attention should be given to feasibility concerns voiced by clinicians.
Accountability and Community on the Internet: A Plea for Restorative Justice
Authors: Kane Laura Wildemann 
Published: April 2020

AbstractIn this article, I analyze norm enforcement on social media, specifically cases where an agent has committed a moral transgression online and is brought to account by an Internet mob with incongruously injurious results in their offline life. I argue that users problematically imagine that they are members of a particular kind of moral community where shaming behaviors are not only acceptable, but morally required to ‘take down’ those who appear to violate community norms. I then demonstrate the costs that are associated with this strategy; the most worrisome being those that distort the nature of moral dialog and the purpose and effectiveness of accountability practices online, creating a vitriolic and polarising online environment. Because of these negative consequences, I suggest that we ought to hold others accountable for restorative ends. I argue that restorative accountability practices can help us cultivate new norms online that rely less for their enforcement upon negative acts such as shame, and more upon positive acts that focus upon the most appropriate way to make amends to the victim(s) and the community. In this sense, restorative accountability incorporates important elements from the ethics of care, a relational ethics that values creating, promoting, and restoring good social and personal relationships. I conclude by arguing that accountability practices premised on the ethics of care produce better outcomes for the victim(s) of a moral violation, the transgressor, and the community.
Effects of self‐management education for persons with Parkinson's disease and their care partners: A qualitative observational study in clinical care
Authors: Hellqvist Carina , Berterö Carina , Hagell Peter , Dizdar Nil , Sund‐Levander Märta 
Published: April 2020

AbstractPersons with Parkinson's disease and their care partners want support from health care to develop the skills to handle everyday life with the long‐term condition. Earlier findings indicate that participants of the self‐management program Swedish National Parkinson School experience several benefits of the program. The purpose of this qualitative observational study was to explore if participants had implemented the strategies of self‐monitoring included in the program and use them to communicate health care status and needs in clinical encounters. Data were collected 3 to 15 months after participation in the program and analyzed using constant comparative analysis. Three categories were evident: “Self‐observation in everyday life,” “Self‐care activities to promote health,” and “Managing emotional impact of Parkinson's Disease.” Categories were linked together in a core category that highlight the use of self‐management strategies described by participants during clinical encounters. Results confirmed that persons with Parkinson's disease and care partners use the techniques of self‐observation in their everyday lives. Observations of effects in clinical care can be a valuable approach to evaluate the outcomes educational interventions and their benefits for individuals and health care.
Aldous Huxley’s search for unity
Authors: Matic Andrija 
Published: April 2020

AbstractEyeless in Gaza (1936) is usually considered Huxley’s most complex work; it makes a break with his social novels of the twenties and establishes him as a proponent of mysticism. However, scholarly analyses of this novel are mostly limited to its non‐linear structure and mystical passages. This paper analyzes epiphanies as important structural and thematic elements of Eyeless in Gaza. Our focus is not only on Anthony Beavis as a protagonist, but also on minor characters such as Helen Ledwidge and Brian Foxe. This paper shows that epiphanies in Eyeless in Gaza anticipate the major ideas of The Perennial Philosophy and The Doors of Perception. We also indicate that Huxley’s use of epiphanies defines his views on Romantic pantheism and positions his literature in the Modernist context.