bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel citation-based search method for scientific literature: a validation study
Authors: Janssens A. Cecile J. W. , Gwinn Marta , Brockman J. Elaine , Powell Kimberley , Goodman Michael 
Published: February 2020

AbstractBackgroundWe recently developed CoCites, a citation-based search method that is designed to be more efficient than traditional keyword-based methods. The method begins with identification of one or more highly relevant publications (query articles) and consists of two searches: the co-citation search, which ranks publications on their co-citation frequency with the query articles, and the citation search, which ranks publications on frequency of all citations that cite or are cited by the query articles.MethodsWe aimed to reproduce the literature searches of published systematic reviews and meta-analyses and assess whether CoCites retrieves all eligible articles while screening fewer titles.ResultsA total of 250 reviews were included. CoCites retrieved a median of 75% of the articles that were included in the original reviews. The percentage of retrieved articles was higher (88%) when the query articles were cited more frequently and when they had more overlap in their citations. Applying CoCites to only the highest-cited article yielded similar results. The co-citation and citation searches combined were more efficient when the review authors had screened more than 500 titles, but not when they had screened less.ConclusionsCoCites is an efficient and accurate method for finding relevant related articles. The method uses the expert knowledge of authors to rank related articles, does not depend on keyword selection and requires no special expertise to build search queries. The method is transparent and reproducible.
Copeptin is independently associated with vascular calcification in chronic kidney disease stage 5
Authors: Golembiewska Edyta , Qureshi Abdul Rashid , Dai Lu , Lindholm Bengt , Heimbürger Olof , Söderberg Magnus , Brismar Torkel B. , Ripsweden Jonaz , Barany Peter , Johnson Richard J. , Stenvinkel Peter 
Published: February 2020

Abstract
Background
Vascular calcification (VC) is an independent predictor of cardiovascular disease (CVD) present in 30–70% of patients with chronic kidney disease (CKD). Copeptin is a sensitive surrogate marker of arginine vasopressin (AVP), which is involved in many pathophysiologic processes in CKD. The aim of the present study was to explore the association of copeptin with VC in CKD stage 5.

Methods
Copeptin was investigated in conjunction with living donor kidney transplantation in 149 clinically stable CKD stage 5 patients (CKD5), including 53 non-dialyzed (CKD5-ND) and 96 dialysis patients treated by peritoneal dialysis (PD) (n = 43) or hemodialysis (HD) (n = 53). We analyzed the association of copeptin with presence and extent of VC ascertained both histologically in biopsies from the inferior epigastric artery (n = 137) and by coronary artery calcification (CAC) score measured by computed tomography.

Results
Patients with higher copeptin were older, had higher systolic blood pressure, higher prevalence of CVD and their preceding time on chronic dialysis was longer. In Spearman’s rank correlations (Rho), copeptin concentrations were significantly associated with CAC score (Rho = 0.27; p = 0.003) and presence of medial VC (Rho = 0.21; p = 0.016). Multivariate logistic regression analysis showed that 1-SD higher age, male gender, diabetes and 1-SD higher copeptin were significantly associated with the presence of moderate-extensive VC.

Conclusions
High circulating levels of copeptin in CKD5 patients are independently associated with the degree of medial calcification ascertained by histology of arterial biopsies. Thus, plasma copeptin may serve as a marker of the uremic calcification process.
Better efficacy in differentiating WHO grade II from III oligodendrogliomas with machine-learning than radiologist’s reading from conventional T1 contrast-enhanced and fluid attenuated inversion recovery images
Authors: Zhao Sha-Sha , Feng Xiu-Long , Hu Yu-Chuan , Han Yu , Tian Qiang , Sun Ying-Zhi , Zhang Jie , Ge Xiang-Wei , Cheng Si-Chao , Li Xiu-Li , Mao Li , Shen Shu-Ning , Yan Lin-Feng , Cui Guang-Bin , Wang Wen 
Published: February 2020

Abstract
Background
The medical imaging to differentiate World Health Organization (WHO) grade II (ODG2) from III (ODG3) oligodendrogliomas still remains a challenge. We investigated whether combination of machine leaning with radiomics from conventional T1 contrast-enhanced (T1 CE) and fluid attenuated inversion recovery (FLAIR) magnetic resonance imaging (MRI) offered superior efficacy.

Methods
Thirty-six patients with histologically confirmed ODGs underwent T1 CE and 33 of them underwent FLAIR MR examination before any intervention from January 2015 to July 2017 were retrospectively recruited in the current study. The volume of interest (VOI) covering the whole tumor enhancement were manually drawn on the T1 CE and FLAIR slice by slice using ITK-SNAP and a total of 1072 features were extracted from the VOI using 3-D slicer software. Random forest (RF) algorithm was applied to differentiate ODG2 from ODG3 and the efficacy was tested with 5-fold cross validation. The diagnostic efficacy of radiomics-based machine learning and radiologist’s assessment were also compared.

Results
Nineteen ODG2 and 17 ODG3 were included in this study and ODG3 tended to present with prominent necrosis and nodular/ring-like enhancement (P < 0.05). The AUC, ACC, sensitivity, and specificity of radiomics were 0.798, 0.735, 0.672, 0.789 for T1 CE, 0.774, 0.689, 0.700, 0.683 for FLAIR, as well as 0.861, 0.781, 0.778, 0.783 for the combination, respectively. The AUCs of radiologists 1, 2 and 3 were 0.700, 0.687, and 0.714, respectively. The efficacy of machine learning based on radiomics was superior to the radiologists’ assessment.

Conclusions
Machine-learning based on radiomics of T1 CE and FLAIR offered superior efficacy to that of radiologists in differentiating ODG2 from ODG3.
Prevalence and associated factors for rural households food insecurity in selected districts of east Gojjam zone, northern Ethiopia: cross-sectional study
Authors: Ayele Amare Wubishet , Kassa Mulusew , Fentahun Yenesew , Edmealem Hayimro 
Published: February 2020

AbstractBackgroundFood insecurity is a pressing social and public health issue that varies in degree and impact on individuals and social groups, requiring immediate attention for policymakers and decision-makers. This study was conducted to identify the prevalence and associated factors of food insecurity of rural households particularly in the Shebel Berenta and Machakel districts of East Gojjam zone.MethodsA cross-sectional study design was conducted, in the fall of March 2017 among 504 households. Households are selected using a systematic sampling technique through multistage cluster sampling technique (two stage cluster sampling). The data were collected using a structured interviewer-administered questionnaire covering a range of topics including 18 core food security modules (CFSM) question series, socioeconomic, demographic and related variables. Multivariable Partial proportional odds model (PPOM) was employed to identify the factors associated with food insecurity in rural households.ResultOf a total of 504 households considered in the study, 54 (10.71%) were highly food secure, 75 (14.88%) were marginally food secure, 157 (31.15%) were low food secure, and 218 (43.25%) were severely food insecure. District (Machakel) (AOR = 3.28 95% CI: 1.73, 6.24), household head education status, illiterate (AOR = 113.4, 95% CI:7.02,1832.02), read and write (AOR = 169.29, 95%CI:11.64, 2461.39), and elementary completed (AOR = 119.75,95%CI:8.43,1700.74), agro-ecological zone, Woina Dega (AOR = 0.0021,95% CI: 0.00009,0.0514), Dega (AOR = 0.0323, 95%CI: 0.002, 0.5209), family size (AOR = 1.18, 95%CI: 1.01, 1.36), landholding (AOR = 0.767, 95% CI: 0.605, 0.972), TLU (AOR = 0.151, 95% CI: 0.0716, 0.3189), access to toilet (no) (AOR = 7.63, 95% CI: 1.459, 39.78), practicing irrigation (yes) (AOR = 0.121, 95% CI: 0.037, 0.38), loan (no) (AOR = 2.83, 95% CI:1.36, 5.89), access to energy, government electric (AOR = 0.468, 95% CI: 0.23, 0.94), solar panels (AOR = 0.45, 95% CI: 0.25, 0.79), soil fertility, moderate (AOR = 0.28, 95% CI: 0.12, 0.87), fertile (AOR = 0.15, 95% CI: 0.032, 0.72) were significant associated food insecurity factors in the study area.ConclusionIn this study, a high prevalence of food insecurity and various associated food insecurity factors have been identified in the study area. Thus, the concerned stockholders should intervene in food insecure households via different irrigation practices and by considering household size, community-based household head education, and landholding in hectare.
A life-threatening complication due to pulmonary haemorrhage following hump-nosed viper bite
Authors: Srirangan Arthihai , Pushpakumara Jagath , Wanigasuriya Kamani 
Published: February 2020

Abstract
Background
Hump-nosed viper bite, the commonest venomous snake bite in Sri Lanka, is associated with significant morbidity. Specific anti-venom is not available for hump-nosed viper envenomation which is usually managed with supportive treatment. Pulmonary haemorrhage is an unusual manifestation of hump-nosed viper bite. Here we present a case of hump-nosed viper envenomation which complicated by pulmonary haemorrhage and was successfully treated with systemic steroids. To the best of our knowledge, it has not been reported in the literature before.

Case presentation
A previously healthy 55-year-old man presented to the local hospital 18 h after a hump-nosed viper bite. He developed bilateral severe pulmonary haemorrhages, evidenced by rapid desaturation which needed intubation and mechanical ventilation, bleeding from the endotracheal tube and bilateral alveolar shadows in a chest x-ray. He had no other bleeding manifestations. Because of the life-threatening situation, he was treated with methylprednisolone pulse therapy. There was a rapid improvement of hypoxia with a resolution of x-ray changes. He was successfully weaned off from the ventilation after 24 h.

Conclusion
This case highlights the importance of suspecting pulmonary haemorrhage in a patient who develops desaturation and alveolar shadow following hump-nosed viper bite even in the absence of other bleeding manifestation. Early and timely treatment with systemic steroid can be lifesaving in such patients.
The Evi5 oncogene promotes laryngeal cancer cells proliferation by stabilizing c-Myc protein
Authors: Mao Cheng-Gang , Zhou Xiao-Chun , Jiang Yi-Dao , Wan Li-Jia , Tao Ze-Zhang , Guo Jun 
Published: February 2020

Abstract
Background
The Ecotropic viral integration site 5 (Evi5) is recognized as a potential oncogene and a cell cycle regulator. Evi5 regulates the abundance of Emi1, an inhibitor of the anaphase-promoting complex/cyclosome, to govern mitotic fidelity. Evi5 has been shown to be dysregulated in several cancer types. However, the expression and biological function of Evi5 in human laryngeal squamous cell carcinoma (LSCC) are still unknown.

Methods
Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing was used to generate Evi5 knockout (KO) LSCC cells. The proliferation and cell cycle distribution of LSCC cells was determined. The effect of Evi5 on LSCC tumor growth in vivo was studied in a tumor xenograft model in mice. The interaction between Evi5 and c-Myc was detected by immunoprecipitation (IP) assay. Luciferase assay was used to determine the transcriptional activity of c-Myc.

Results
Here, we show that Evi5 controls LSCC tumorigenesis via the stabilization of c-MYC oncogene. CRISPR-mediated knockout (KO) of Evi5 decreased the proliferation and decreased colony formation ability of LSCC cells. Knockout of Evi5 caused increased G1 phase and decreased S phase cells. In the tumor-bearing nude mice, The transplanted tumors originated from Evi5-KO TU212 cells were significantly decreased when compared with control TU212 cells. At the molecular level, we found that Evi5 interacted with c-MYC and Evi5 antagonized E3 ligase FBXW7-mediated ubiquitination and degradation of c-Myc protein, and promoted c-Myc-dependent transactivation.

Conclusion
Given the critical role of c-Myc in tumorigenesis, our data suggest that Evi5 is a potential therapeutic target in LSCC, and inhibition of Evi5 should be a prospective strategy for LSCC therapy.
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
Authors: Qin Qian , Fan Jingyu , Zheng Rongbin , Wan Changxin , Mei Shenglin , Wu Qiu , Sun Hanfei , Brown Myles , Zhang Jing , Meyer Clifford A. , Liu X. Shirley 
Published: February 2020

AbstractWe developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes and outperformed alternative methods in identifying the perturbed TRs.
Purifying selection of long dsRNA is the first line of defense against false activation of innate immunity
Authors: Barak Michal , Porath Hagit T. , Finkelstein Gilad , Knisbacher Binyamin A. , Buchumenski Ilana , Roth Shalom Hillel , Levanon Erez Y. , Eisenberg Eli 
Published: February 2020

Abstract
Background
Mobile elements comprise a large fraction of metazoan genomes. Accumulation of mobile elements is bound to produce multiple putative double-stranded RNA (dsRNA) structures within the transcriptome. These endogenous dsRNA structures resemble viral RNA and may trigger false activation of the innate immune response, leading to severe damage to the host cell. Adenosine to inosine (A-to-I) RNA editing is a common post-transcriptional modification, abundant within repetitive elements of all metazoans. It was recently shown that a key function of A-to-I RNA editing by ADAR1 is to suppress the immunogenic response by endogenous dsRNAs.

Results
Here, we analyze the transcriptomes of dozens of species across the Metazoa and identify a strong genomic selection against endogenous dsRNAs, resulting in their purification from the canonical transcriptome. This purifying selection is especially strong for long and nearly perfect dsRNAs. These are almost absent from mRNAs, but not pre-mRNAs, supporting the notion of selection due to cytoplasmic processes. The few long and nearly perfect structures found in human transcripts are weakly expressed and often heavily edited.

Conclusion
Purifying selection of long dsRNA is an important defense mechanism against false activation of innate immunity. This newly identified principle governs the integration of mobile elements into the genome, a major driving force of genome evolution. Furthermore, we find that most ADAR1 activity is not required to prevent an immune response to endogenous dsRNAs. The critical targets of ADAR1 editing are, likely, to be found mostly in non-canonical transcripts.
Transcriptomics of Gabra4 knockout mice reveals common NMDAR pathways underlying autism, memory, and epilepsy
Authors: Fan Cuixia , Gao Yue , Liang Guanmei , Huang Lang , Wang Jing , Yang Xiaoxue , Shi Yiwu , Dräger Ursula C. , Zhong Mei , Gao Tian-Ming , Yang Xinping 
Published: February 2020

AbstractAutism spectrum disorder (ASD) is a neuronal developmental disorder with impaired social interaction and communication, often with abnormal intelligence and comorbidity with epilepsy. Disturbances in synaptic transmission, including the GABAergic, glutamatergic, and serotonergic systems, are known to be involved in the pathogenesis of this disorder, yet we do not know if there is a common molecular mechanism. As mutations in the GABAergic receptor subunit gene GABRA4 are reported in patients with ASD, we eliminated the Gabra4 gene in mice and found that the Gabra4 knockout mice showed autistic-like behavior, enhanced spatial memory, and attenuated susceptibility to pentylenetetrazol-induced seizures, a constellation of symptoms resembling human high-functioning autism. To search for potential molecular pathways involved in these phenotypes, we performed a hippocampal transcriptome profiling, constructed a hippocampal interactome network, and revealed an upregulation of the NMDAR system at the center of the converged pathways underlying high-functioning autism-like and anti-epilepsy phenotypes.
Different approaches for transformation of mesenchymal stem cells into hepatocyte-like cells
Authors: Afshari Afsoon , Shamdani Sara , Uzan Georges , Naserian Sina , Azarpira Negar 
Published: February 2020

AbstractDue to the prominent role of the liver in the body and detoxification, its functionality can be affected in an irreversible manner by diseases. This phenomenon renders the liver to stop working, leading to morbidity and mortality. Therefore, liver transplantation is the only way to tackle this issue.In order to compensate for the lack of adequate healthy liver tissue for transplantation, therapeutic approaches such as hepatocyte transplantation have been proposed as an alternative. Recognizing the fact that mesenchymal stem cells are adult stem cells with the capacity to differentiate into several cell types, different methods have been invented to produce hepatocyte-like cells from mesenchymal stem cells. They can be divided into three main categories, such as addition of cytokines and growth factors, genetic modifications, and adjustment of microenvironment as well as physical parameters.In this review, we attempted to introduce diverse efficient methods for differentiating mesenchymal stem cells and their capability for transformation into hepatocyte-like cells.
Infusion-related thrombogenesis by liver-derived mesenchymal stem cells controlled by anticoagulant drugs in 11 patients with liver-based metabolic disorders
Authors: Coppin Louise C. F. , Smets Françoise , Ambroise Jérome , Sokal Etienne E. M. , Stéphenne Xavier 
Published: February 2020

Abstract
Background
Mesenchymal stem cell (MSC) transplantation is a fast-developing therapy in regenerative medicine. However, some concerns have been raised regarding their safety and the infusion-related pro-coagulant activity. The aim of this study is to analyze the induced thrombogenic risk and the safety of adding anticoagulants during intraportal infusions of liver-derived MSCs (HepaStem), in patients with Crigler-Najjar (CN) and urea cycle disorders (UCD).

Methods
Eleven patients (6 CN and 5 UCD patients) were included in this partially randomized phase 1/2 study. Three cell doses of HepaStem were investigated: low (12.5 × 106 cells/kg), intermediate (50 × 106 cells/kg), and high doses (200 × 106 cells/kg). A combination of anticoagulants, heparin (10 I.U./5 × 106cells), and bivalirudin (1.75 mg/kg/h) were added during cell infusions. The infusion-related thrombogenic risk and anticoagulation were evaluated by clinical monitoring, blood sampling (platelet and D-dimer levels, activated clotting time, etc.) and liver Doppler ultrasound. Mixed effects linear regression models were used to assess statistically significant differences.

Results
One patient presented a thrombogenic event such as a partial portal vein thrombus after 6 infusions. Minor adverse effects such as petechiae, epistaxis, and cutaneous hemorrhage at the site of catheter placement were observed in four patients. A significant decrease in platelet and increase in D-dimer levels were observed at the end of the infusion cycle, normalizing spontaneously after 7 days. No significant and clinically relevant increase in portal vein pressure could be observed once the infusion cycle was completed.

Conclusions
The safety- and the infusion-related pro-coagulant activity remains a concern in MSC transplantation. In our study, a combination of heparin and bivalirudin was added to prevent the thrombogenic risk induced by HepaStem infusions in 11 patients. A significant decrease in platelet and increase in D-dimer levels were observed, suggesting the activation of coagulation in these patients; however, this was spontaneously reversible in time. We can conclude that adding this combination of anticoagulants is safe and limits infusion-related thrombogenesis to subclinical signs in most of the patients.

Trial registration
ClinicalTrials.gov identifier: NCT01765283—January 10, 2013
Application of supervised descent method for 2D magnetotelluric data inversion
Authors: Guo Rui , Li Maokun , Yang Fan , Xu Shenheng , Abubakar Aria 
Published: February 2020

The supervised descent method (SDM) is applied to 2D magnetotellurics (MT) data inversion. SDM contains offline training and online prediction. The training set is composed of the models generated according to prior knowledge and the data simulated by MT forward modeling. In the training process, a set of descent directions from an initial model to the training models is learned. In the prediction, model reconstruction is achieved by optimizing an online regularized objective function with a restart scheme, where the learned descent directions and the computed data residual are involved. SDM inversion has the advantages of (1) being more efficient than traditional gradient-descent methods because the computation of local derivatives of the objective function is avoided, (2) incorporating prior uncertain knowledge easier than deterministic inversion approach by generating training models flexibly, and (3) having high generalization ability because the physical modeling can guide the online model reconstruction. Furthermore, a way of designing general training set is introduced, which can be used for training when the prior knowledge is weak. The efficiency and accuracy of this method are validated by two numerical examples. The results indicate that the reconstructed models are consistent with prior information, and the simulated responses agree well with the data. This method also shows good potential to improve the accuracy and efficiency in field MT data inversion.