bluuebunny/crossref_metadata_2025_split huggingface dataset:
An automatic hypothesis generation for plausible linkage between xanthium and diabetes
Authors: Syafiandini Arida Ferti , Song Gyuri , Ahn Yuri , Kim Heeyoung , Song Min 
Published: October 2022

AbstractThere has been a significant increase in text mining implementation for biomedical literature in recent years. Previous studies introduced the implementation of text mining and literature-based discovery to generate hypotheses of potential candidates for drug development. By conducting a hypothesis-generation step and using evidence from published journal articles or proceedings, previous studies have managed to reduce experimental time and costs. First, we applied the closed discovery approach from Swanson’s ABC model to collect publications related to 36 Xanthium compounds or diabetes. Second, we extracted biomedical entities and relations using a knowledge extraction engine, the Public Knowledge Discovery Engine for Java or PKDE4J. Third, we built a knowledge graph using the obtained bio entities and relations and then generated paths with Xanthium compounds as source nodes and diabetes as the target node. Lastly, we employed graph embeddings to rank each path and evaluated the results based on domain experts’ opinions and literature. Among 36 Xanthium compounds, 35 had direct paths to five diabetes-related nodes. We ranked 2,740,314 paths in total between 35 Xanthium compounds and three diabetes-related phrases: type 1 diabetes, type 2 diabetes, and diabetes mellitus. Based on the top five percentile paths, we concluded that adenosine, choline, beta-sitosterol, rhamnose, and scopoletin were potential candidates for diabetes drug development using natural products. Our framework for hypothesis generation employs a closed discovery from Swanson’s ABC model that has proven very helpful in discovering biological linkages between bio entities. The PKDE4J tools we used to capture bio entities from our document collection could label entities into five categories: genes, compounds, phenotypes, biological processes, and molecular functions. Using the BioPREP model, we managed to interpret the semantic relatedness between two nodes and provided paths containing valuable hypotheses. Lastly, using a graph-embedding algorithm in our path-ranking analysis, we exploited the semantic relatedness while preserving the graph structure properties.
Identification of a novel ceRNA network related to prognosis and immunity in HNSCC based on integrated bioinformatic investigation
Authors: Liu Hongbo , Hei Guoli , Zhang Lu , Jiang Yanxia , Lu Haijun 
Published: October 2022

AbstractHead and neck squamous cell carcinoma (HNSCC) is characterized by an immunosuppression environment and necessitates the development of new immunotherapy response predictors. The study aimed to build a prognosis-related competing endogenous RNA (ceRNA) network based on immune-related genes (IRGs) and analyze its immunological signatures. Differentially expressed IRGs were identified by bioinformatics analysis with Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and ImmPort databases. Finally, via upstream prognosis-related microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) prediction and co-expression analysis, we built an immune-related ceRNA network (LINC00052/hsa-miR-148a-3p/PLAU) related to HNSCC patient prognosis. CIBERSORT analysis demonstrated that there were substantial differences in 11 infiltrating immune cells in HNSCC, and PLAU was closely correlated with 10 type cells, including T cells CD8+ (R =  − 0.329), T cells follicular helper (R = − 0.342) and macrophage M0 (R = 0.278). Methylation and Tumor Immune Dysfunction and Exclusion (TIDE) analyses revealed that PLAU upregulation was most likely caused by hypomethylation and that high PLAU expression may be associated with tumor immune evasion in HNSCC, respectively.
Automatic deep learning-based consolidation/collapse classification in lung ultrasound images for COVID-19 induced pneumonia
Authors: Durrani Nabeel , Vukovic Damjan , van der Burgt Jeroen , Antico Maria , van Sloun Ruud J. G. , Canty David , Steffens Marian , Wang Andrew , Royse Alistair , Royse Colin , Haji Kavi , Dowling Jason , Chetty Girija , Fontanarosa Davide 
Published: October 2022

AbstractOur automated deep learning-based approach identifies consolidation/collapse in LUS images to aid in the identification of late stages of COVID-19 induced pneumonia, where consolidation/collapse is one of the possible associated pathologies. A common challenge in training such models is that annotating each frame of an ultrasound video requires high labelling effort. This effort in practice becomes prohibitive for large ultrasound datasets. To understand the impact of various degrees of labelling precision, we compare labelling strategies to train fully supervised models (frame-based method, higher labelling effort) and inaccurately supervised models (video-based methods, lower labelling effort), both of which yield binary predictions for LUS videos on a frame-by-frame level. We moreover introduce a novel sampled quaternary method which randomly samples only 10% of the LUS video frames and subsequently assigns (ordinal) categorical labels to all frames in the video based on the fraction of positively annotated samples. This method outperformed the inaccurately supervised video-based method and more surprisingly, the supervised frame-based approach with respect to metrics such as precision-recall area under curve (PR-AUC) and F1 score, despite being a form of inaccurate learning. We argue that our video-based method is more robust with respect to label noise and mitigates overfitting in a manner similar to label smoothing. The algorithm was trained using a ten-fold cross validation, which resulted in a PR-AUC score of 73% and an accuracy of 89%. While the efficacy of our classifier using the sampled quaternary method significantly lowers the labelling effort, it must be verified on a larger consolidation/collapse dataset, our proposed classifier using the sampled quaternary video-based method is clinically comparable with trained experts’ performance.
Contribution of CRISPRable DNA to human complex traits
Authors: Zhai Ranran , Zheng Chenqing , Yang Zhijian , Li Ting , Chen Jiantao , Shen Xia 
Published: October 2022

AbstractCRISPR-Cas is a powerful genome editing tool for various species and human cell lines, widely used in many research areas including studying the mechanisms, targets, and gene therapies of human diseases. Recent developments have even allowed high-throughput genetic screening using the CRISPR system. However, due to the practical and ethical limitations in human gene editing research, little is known about whether CRISPR-editable DNA segments could influence human complex traits or diseases. Here, we investigated the human genomic regions condensed with different CRISPR Cas enzymes’ protospacer-adjacent motifs (PAMs). We found that Cas enzymes with GC-rich PAMs could interfere more with the genomic regions that harbor enriched heritability for human complex traits and diseases. The results linked GC content across the genome to the functional genomic elements in the heritability enrichment of human complex traits. We provide a genetic overview of the effects of high-throughput genome editing on human complex traits.
Bipolar cell targeted optogenetic gene therapy restores parallel retinal signaling and high-level vision in the degenerated retina
Authors: Kralik Jakub , van Wyk Michiel , Stocker Nino , Kleinlogel Sonja 
Published: October 2022

AbstractOptogenetic gene therapies to restore vision are in clinical trials. Whilst current clinical approaches target the ganglion cells, the output neurons of the retina, new molecular tools enable efficient targeting of the first order retinal interneurons, the bipolar cells, with the potential to restore a higher quality of vision. Here we investigate retinal signaling and behavioral vision in blind mice treated with bipolar cell targeted optogenetic gene therapies. All tested tools, including medium-wave opsin, Opto-mGluR6, and two new melanopsin based chimeras restored visual acuity and contrast sensitivity. The best performing opsin was a melanopsin-mGluR6 chimera, which in some cases restored visual acuities and contrast sensitivities that match wild-type animals. Light responses from the ganglion cells were robust with diverse receptive-field types, inferring elaborate inner retinal signaling. Our results highlight the potential of bipolar cell targeted optogenetics to recover high-level vision in human patients with end-stage retinal degenerations.
Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea
Authors: Shao Nana , Fan Yu , Chou Chau-Wen , Yavari Shadi , Williams Robert V. , Amster I. Jonathan , Brown Stuart M. , Drake Ian J. , Duin Evert C. , Whitman William B. , Liu Yuchen 
Published: October 2022

AbstractMethanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.
Stronger adaptive response among small-scale fishers experiencing greater climate change hazard exposure
Authors: Ilosvay Xochitl Édua Elías , Molinos Jorge García , Ojea Elena 
Published: October 2022

AbstractProgressive climate-driven environmental changes are threatening the global livelihoods of small-scale fishers, yet how their adaptation responses vary in relation to hazard exposure is poorly understood. We use a systematic review approach to identify a global data set of 301 reported adaptation responses (remaining, adaptive, and transformative) of small-scale fishers to climate change and analyse their spatial agreement with estimated geographical location of global coastal hotspot areas for specific climate change hazards associated to those responses (long-term trends in sea surface temperature, cumulative intensity of marine heatwaves, frequency of tropical storms, and intensity of associated storm surges). Only 37% of responses were found in climate change hotspots. Despite this, our results evidence that fishers are responding more passively in areas with lower exposure levels to abrupt climatic events. The relative proportion of adaptive and transformative responses increase with climate change hazard exposure.
Impulsively generated two-fluid magnetoacoustic-gravity waves: Solar chromosphere heating and plasma outflows
Authors: Niedziela R. , Murawski K. , Kadowaki L. , Zaqarashvili T. , Poedts S. 
Published: October 2022

Context. We use a two-fluid model to study the heating of the solar chromosphere by magnetoacoustic and magnetoacoustic-gravity waves. In the model, we include energy dissipation as a result of ion–neutral collisions.
Aims. The aim of this paper is to study impulsively generated two-fluid magnetoacoustic and magnetoacoustic-gravity waves and to quantify their contribution to chromosphere heating and the generation of plasma outflows.
Methods. We consider a 2D model of the gravitationally stratified and partially ionized solar atmosphere that is permeated by a vertical magnetic field. To describe the dynamics of the atmosphere, we use a set of two-fluid equations which we solve numerically with the use of the JOANNA code.
Results. We show that large-amplitude impulsively generated magnetoacoustic-gravity waves can efficiently heat the chromosphere and generate plasma outflows in the low solar corona. The chromosphere is heated by ion–neutral collisions, which are most effective at the top of this atmospheric layer. Wider and larger amplitude pulses heat the atmosphere more effectively and generate faster plasma outflows.
Conclusions. Large-amplitude, impulsively generated two-fluid magnetoacoustic-gravity waves have the potential to contribute to the solar chromosphere heating and plasma outflows in the low corona.
The Application of 2-Naphthols in Asymmetric Synthesis of Atropisomers
Authors: Xiang Shao-Hua , Cheng Jun Kee , Tan Bin 
Published: October 2022

AbstractThe venerable axially chiral biaryl skeletons used widely in asymmetric catalysis such as BINOLs, NOBINs, QUINOLs, and CPAs possess a 2-naphthol moiety or are derived from the naphthol precursor. The hydroxy functionality offers the interaction point or serves as functional handle for synthetic elaboration. This prevalence and significance drive our studies to incorporate this nucleophile class to fabricate an assortment of atropisomers. By activating the reacting partners via distinctive mechanisms, the arylation of quinones, azo- or nitroso-naphthalenes, VQM intermediates, 1,2,4-triazole-3,5-diones, isoquinolines, and 1-bromo-2-naphthols with 2-naphthols were successfully attained. A concise account of these developments is provided in this article.1	Introduction2	Asymmetric Arylation with Quinones3	Asymmetric Arylation with Electron-Deficient Arenes4	Asymmetric Synthesis of Atropisomers with other Electrophiles5	Conclusion
Prevalence of Dyslipidemia among School-Age Children and Adolescents in Addis Ababa, Ethiopia
Authors: Mohammed Ousman , Kassaw Melkitu , G/Egzeabher Letebrhan , Fekadu Endalkachew , Bikila Demiraw , Getahun Tigist , Challa Feyissa , Abdu Ahmedmenewer , Desta Kassu , Wolde Mistire , Tsegaye Aster 
Published: October 2022

Abstract
Objective Lipid abnormalities during childhood might be associated with a higher risk of atherosclerosis development in adulthood. In Ethiopia, there were no data on this area. The present work was aimed at assessing the lipid profile abnormalities among children and adolescents aged between 5 and 17 years, in Addis Ababa, Ethiopia.
Materials and Methods The present school-based cross-sectional study was done from March 2019 to October 2019 in the capital city, Addis Ababa. A total of 504 students were randomly recruited for this study. The total cholesterol, triglyceride, low-density lipoprotein, and high-density lipoprotein-cholesterol levels were determined using the Cobas c501 automated chemistry analyzer. The prevalence of lipid abnormalities was described in percentages. Bivariate and multivariate analyses were performed, and data with p-value less than 0.05 was considered statistically significant.
Results Dyslipidemia in at least one of the lipid profiles was observed in 322 (63.9%) school children, whereas only one of the participants had an abnormality in all four lipid profile tests. The prevalence of total cholesterol 200 mg/dL or higher, low-density lipoprotein 130 mg/dL or higher, high-density lipoprotein less than 40 mg/dL, and triglycerides 130 mg/dL or higher was in 14 (2.8%), 16 (3.2%), 294 (58.4%), and 46 (19.1%) participants, respectively.
Conclusion In the current work, the majority of the study participants had a normal lipid profile except increased prevalence of a reduced concentration of high-density lipoprotein-cholesterol. The overall prevalence of serum lipid abnormalities was 63.9%. Serum lipid levels did not show significant differences with sex, age, fasting habits, or obesity.
Correlation of Thrombosis and Clinicohematological Parameters with JAK2V617F Mutation in Philadelphia-Negative CMPNs: A Study from India
Authors: Singh Kanwaljeet , V. Pradeep , Ahuja Ankur , Somasundarum Venkatesan , Mishra Kundan , Chatterjee Tathagat 
Published: October 2022

Abstract
Objective Philadelphia-negative chronic myeloproliferative neoplasms (CMPNs), which include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), are characterized by the presence of JAK2V617F (exon 14) mutation, and this occurs in 90 to 95% cases of PV and 50 to 60% cases of ET and PMF. Still, this is a matter of debate regarding the correlation of this mutation with thrombosis and clinicohematological parameters in CMPNs. So, we conducted this study to ascertain the association of JAK2V617F mutation with thrombotic complications and clinicohematological parameters of these patients.
Materials and Methods This prospective and retrospective study was conducted during 2018 to 2019 at the Department of Laboratory Sciences and Molecular Medicine of a tertiary care hospital, and 160 CMPN patients were enrolled. Complete hemogram was done and DNA was extracted, followed by real-time qualitative polymerase chain reaction to check for JAK2V617F mutation. This mutation was then correlated with complications, mainly thrombosis, hematological parameters, and clinical parameters such as age and splenomegaly.
Results Among 160 CMPN patients, 60 were females and 100 were males, with male to female ratio of 1:0.6, and age range of 27 to 85 years. Total 91 (56.9%) patients were JAK2V617F positive and the remaining 69 (43.1%) were negative for this mutation. We observed statistically significant correlation of leukocyte count, splenomegaly, and thrombosis in JAK2V617F-mutated patients as compared to unmutated patients.
Conclusion This study emphasizes the importance of JAK2V617F mutation in CMPNs and stresses on its association with clinical, hematological phenotype, and thrombotic complications, which may open new horizons in prognostication and management protocol.
Pure Red Cell Aplasia Encountered in a Tertiary Care Hematology Laboratory: A Series of Nine Distinctive Cases
Authors: Kala Mansi , Das Kunal , Baveja Avriti , Raturi Manish , Dhebane Meghali , Ahmad Sohaib , Mehrotra Mansi 
Published: October 2022

AbstractPure red cell aplasia (PRCA) is characterized by severe anemia with reticulocytopenia and bone marrow erythroblastopenia. The early erythroblasts are markedly decreased; however, in rare instances, they may be normal or raised in number. There are varied etiologies, namely congenital or acquired and primary or secondary. The congenital PRCA is known as “Diamond-Blackfan anemia.” Thymomas, autoimmune disease, lymphomas, infections, and drugs also may be familiar associates. However, the etiologies of PRCA are numerous, and many diseases/infections can be associated with PRCA. The diagnosis rests on clinical suspicion and appropriate laboratory workup. We evaluated nine cases of red cell aplasia, having severe anemia with reticulocytopenia. Nearly half of the cases showed adequate erythroid (> 5% of the differential count) but with a maturation arrest. The adequacy of the erythroid could confuse the hematologist and may even delay the diagnosis. Hence, it is empirical that PRCA could be considered a differential in every case of severe anemia with reticulocytopenia, even in the presence of adequate erythroid precursors in the bone marrow.
Phase Transition Enthalpy Measurements of Organic Compounds. An Update of Sublimation, Vaporization, and Fusion Enthalpies from 2016 to 2021
Authors: Acree William , Chickos James S. 
Published: October 2022

The compendium of phase change enthalpies published in two parts in 2016 is updated to include new fusion, vaporization, and sublimation enthalpies published in the interim and includes some earlier data either previously missed or were unavailable. Also included in this article is an update of recent studies on the phase change enthalpies of polyaromatic hydrocarbons. Group values previously evaluated to adjust for temperature of phase changes are updated for aromatic compounds in view of recent experimental data. The new group parameters have been evaluated on the basis of their consistency in providing appropriate temperature adjustments to phase change enthalpies at T = 298 K as evaluated by a thermochemical cycle. This evaluation provides transition temperatures and about 1000 heats of fusion, 700 heats of vaporization, 500 heats of sublimation, and about 50 other heats of transitions for about 30 polyaromatic hydrocarbons and 1100 other molecules consisting of C1-C57 organic compunds, organometallics, inorganic compounds, and ionic liquids taken from about 900 references.
Changes in paediatric Ambulatory Care Sensitive Conditions in Victoria, 2018–20: the COVID-19 effect?
Authors: White Mary , Craig Simon , Chu Wanyu , Hiscock Harriet 
Published: October 2022

Objectives This study sought to describe the patterns in emergency department (ED) presentations and hospital admissions in children with Ambulatory Care Sensitive Conditions (ACSCs) before and during the coronavirus disease 2019 (COVID-19) pandemic restrictions in Victoria, Australia, to assess if changes in out-of-hospital care resulted in an increase in delayed/severe presentations. Methods This study involved secondary analysis of Victorian Emergency Minimum Dataset and Victorian Admitted Episode Dataset data. Patients (<18 years) attending EDs with a diagnosis of an ACSC were included. We compared the number and severity of ASCS presentations pre-COVID-19 (1January 2018–27 March 2020) and during COVID-19 (28 March–31 October 2020). A linear regression prediction model was built to compare the observed versus predicted presentation number in the 2020 period. Results In total, there were 108 104 paediatric ACSC ED presentations in Victoria during the study period. Females accounted for 51 462/108 104 (47.6%) of all presentations, with a median age of 3 years. A significant decrease in ED presentations was seen in 2020 (41 319 in 2018; 44 978 in 2019; and 21 807 until October 2020), predominantly due to reductions in conditions that are typically mediated by viruses in childhood (i.e. asthma, convulsions/epilepsy and ear, nose and throat conditions). The proportion of high-urgency presentations and those requiring admission was stable in 2020. Conclusions An overall reduction in the number of ED presentations and admissions with paediatric ACSCs was seen in Victoria in 2020, indicating that rates of delayed or more severe presentations did not occur as a result of changes in out-of-hospital care.
“I know how you feel”
Authors: Andriella Antonio , Huertas-Garcia Ruben , Forgas-Coll Santiago , Torras Carme , Alenyà Guillem 
Published: October 2022

Abstract
In this article, we aim to evaluate the role of robots’ personality-driven behavioural patterns on users’
intention to use in an entertainment scenario. Toward such a goal, we designed two personalities: one introverted with an empathic
and self-comparative interaction style, and the other extroverted with a provocative and other-comparative interaction style. To
evaluate the proposed technology acceptance model, we conducted an experiment (N = 209) at a public venue where
users were requested to play a game with the support of the TIAGo robot. Our findings show that the robot personality affects the
acceptance model and three relevant drivers: perceived enjoyment, perceived usefulness, and social influence. The extroverted
robot was perceived as more useful than the introverted, and participants who interacted with it were faster at solving the game.
On the other hand, the introverted robot was perceived as more enjoyable but less useful than the extroverted, and participants
who interacted with it made fewer mistakes. Taken together, these findings support the importance of designing proper robot
personalities in influencing users’ acceptance, featuring that a given style can elicit a different driver of acceptance.