bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database
Authors: Korn Daniel , Bobrowski Tesia , Li Michael , Kebede Yaphet , Wang Patrick , Owen Phillips , Vaidya Gaurav , Muratov Eugene , Chirkova Rada , Bizon Chris , Tropsha Alexander 
Published: November 2020

Abstract

Summary
In response to the COVID-19 pandemic, we established COVID-KOP, a new knowledgebase integrating the existing Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP) biomedical knowledge graph with information from recent biomedical literature on COVID-19 annotated in the CORD-19 collection. COVID-KOP can be used effectively to generate new hypotheses concerning repurposing of known drugs and clinical drug candidates against COVID-19 by establishing respective confirmatory pathways of drug action.

Availability and implementation
COVID-KOP is freely accessible at https://covidkop.renci.org/. For code and instructions for the original ROBOKOP, see: https://github.com/NCATS-Gamma/robokop.
Semiparametric regression on cumulative incidence function with interval-censored competing risks data and missing event types
Authors: Park Jun , Bakoyannis Giorgos , Zhang Ying , Yiannoutsos Constantin T 
Published: November 2020

Summary
Competing risk data are frequently interval-censored, that is, the exact event time is not observed but only known to lie between two examination time points such as clinic visits. In addition to interval censoring, another common complication is that the event type is missing for some study participants. In this article, we propose an augmented inverse probability weighted sieve maximum likelihood estimator for the analysis of interval-censored competing risk data in the presence of missing event types. The estimator imposes weaker than usual missing at random assumptions by allowing for the inclusion of auxiliary variables that are potentially associated with the probability of missingness. The proposed estimator is shown to be doubly robust, in the sense that it is consistent even if either the model for the probability of missingness or the model for the probability of the event type is misspecified. Extensive Monte Carlo simulation studies show good performance of the proposed method even under a large amount of missing event types. The method is illustrated using data from an HIV cohort study in sub-Saharan Africa, where a significant portion of events types is missing. The proposed method can be readily implemented using the new function ciregic_aipw in the R package intccr.
Susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Children and Adults: A Seroprevalence Study of Family Households in the Barcelona Metropolitan Region, Spain
Authors: Brotons Pedro , Launes Cristian , Buetas Elena , Fumado Vicky , Henares Desiree , de Sevilla Mariona Fernandez , Redin Alba , Fuente-Soro Laura , Cuadras Daniel , Mele Maria , Jou Cristina , Millat Pere , Jordan Iolanda , Garcia-Garcia Juan Jose , Bassat Quique , Muñoz-Almagro Carmen ,   Kids Corona Study Group, Adroher Cristina , Alsina Laia , Ajanovic Sara , Andueza Ainhoa , Arias Sara , Balanza Nuria , Baro Barbara , Bonet-Carne Elisenda , Claverol Joana , Cubells Marta , Fortuny Claudia , Garcia-Miguel Aleix , Gratacos Eduard , Hernandez Maria , Morales Monica , Pérez-Soler Felipe , Ríos María , Millat Pere , Pons Gemma , Torrents Francesc , Uribesalgo Iris , Valls Anna , Varo Rosauro 
Published: November 2020

Abstract

Background
Susceptibility of children and adults to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and persistence of antibody response to the virus after infection resolution remain poorly understood, despite their significant public health implications.

Methods
A prospective cross-sectional seroprevalence study with volunteer families that included at least 1 first-reported adult case positive by SARS-CoV-2 by polymerase chain reaction (PCR) and at least 1 child aged &lt;15 years living in the same household under strict home confinement was conducted in the metropolitan Barcelona Health Region, Spain, during the pandemic period 28 April 2020–3 June 2020. All household members were tested at home using a rapid SARS-CoV-2 antibody assay with finger prick–obtained capillary blood.

Results
A total of 381 family households including 381 first-reported PCR-positive adult cases and 1084 contacts (672 children, 412 adults) were enrolled. SARS-CoV-2 seroprevalence rates were 17.6% (118 of 672) in children and 18.7% (77 of 335) in adult contacts (P = .64). Among first-reported cases, seropositivity rates varied from 84.0% in adults previously hospitalized and tested within 6 weeks since the first positive PCR result to 31.5% in those not hospitalized and tested after that lag time (P &lt; .001). Nearly all (99.9%) positive children were asymptomatic or had mild symptoms.

Conclusions
Children appear to have similar probability as adults to become infected by SARS-CoV-2 in quarantined family households but remain largely asymptomatic. Adult antibody protection against SARS-CoV-2 seems to be weak beyond 6 weeks post-infection confirmation, especially in cases that have experienced mild disease.
Establishing a New Normal for Hospital Care: A Whole of Hospital Approach to Coronavirus Disease 2019 (COVID-19)
Authors: Lum Brandon X , Liu Eugene H , Archuleta Sophia , Somani Jyoti , Bagdasarian Natasha , Koh Catherine S , Sin Clara S , Wong Mushan , Quek Swee Chye , Fisher Dale A 
Published: November 2020

AbstractSingapore’s hospitals had prepared to receive patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), planning various scenarios and levels of surge with a policy of isolating all confirmed cases as inpatients. The National University Hospital adopted a whole of hospital approach to coronavirus disease 2019 (COVID-19) with 3 primary goals: zero hospital-acquired COVID-19, all patients receive timely necessary care, and maintenance of staff morale. These goals to date have been met. A large influx of COVID-19 cases required significant transformation of clinical and operational processes. Isolation room numbers almost tripled and dedicated COVID-19 cohort wards were established, elective care was postponed, and intensive care units were augmented with equipment and manpower. In the wake of the surge, establishing a new normal for hospital care requires maintaining vigilance to detect endemic COVID-19, establishing contingency plans to ramp up in case of another surge, while returning to business as usual.
Genomic characterization of the adolescent idiopathic scoliosis-associated transcriptome and regulome
Authors: Makki Nadja , Zhao Jingjing , Liu Zhaoyang , Eckalbar Walter L , Ushiki Aki , Khanshour Anas M , Wu Joe , Rios Jonathan , Gray Ryan S , Wise Carol A , Ahituv Nadav 
Published: November 2020

Abstract
Adolescent idiopathic scoliosis (AIS), a sideways curvature of the spine, is the most common pediatric musculoskeletal disorder, affecting ~3% of the population worldwide. However, its genetic bases and tissues of origin remain largely unknown. Several genome-wide association studies (GWAS) have implicated nucleotide variants in non-coding sequences that control genes with important roles in cartilage, muscle, bone, connective tissue and intervertebral disks (IVDs) as drivers of AIS susceptibility. Here, we set out to define the expression of AIS-associated genes and active regulatory elements by performing RNA-seq and chromatin immunoprecipitation-sequencing against H3 lysine 27 acetylation in these tissues in mouse and human. Our study highlights genetic pathways involving AIS-associated loci that regulate chondrogenesis, IVD development and connective tissue maintenance and homeostasis. In addition, we identify thousands of putative AIS-associated regulatory elements which may orchestrate tissue-specific expression in musculoskeletal tissues of the spine. Quantification of enhancer activity of several candidate regulatory elements from our study identifies three functional enhancers carrying AIS-associated GWAS SNPs at the ADGRG6 and BNC2 loci. Our findings provide a novel genome-wide catalog of AIS-relevant genes and regulatory elements and aid in the identification of novel targets for AIS causality and treatment.
Dual Nationality of a Private Investor in Investment Treaty Arbitration: A Potential Barrier to the Exercise of Jurisdiction Ratione Personae?
Authors: Vijayvergia Chitransh 
Published: November 2020

Abstract
One of the fundamental objectives of international investment agreements (IIAs) is to protect the rights and interests of foreign investors in the territory of a contracting State. Why, then, have tribunals often exercised jurisdiction ratione personae over the claims of dual nationals against their own State? The answer lies in the silence of IIAs on the matter of dual nationals. Such agreements have failed expressly to mention dual nationals in their definitions of ‘investor’ or ‘national’, which has created lacunae that are open to interpretation. Tribunals have often fallen back on international law to fill these gaps and accurately to determine the nationality of an investor’s claims. They have taken into consideration the text of the IIAs, the text of institutional rules and the general principles of international law. The principle of ‘dominant and effective nationality’, as propounded in the Nottebohm case, has made frequent appearances in such interpretation processes. However, the application of this principle has been inconsistent over time, with different tribunals taking different stances. In this article, the author traces this varied approaches of tribunals. In doing so, he analyses the text of and the awards delivered in disputes arising out of the Algiers Declaration, the North American Free Trade Agreement (NAFTA), the United States–Mexico–Canada Agreement (USMCA), the Convention on the Settlement of Investment Disputes between States and Nationals of Other States (ICSID Convention), the Dominican Republic–Central America Free Trade Agreement (DR-CAFTA), the United Nations Commission on International Trade Law (UNCITRAL) Arbitration Rules and various bilateral investment treaties (BITs). Based on this analysis, the author proposes several changes that States should consider in the future negotiation of BITs to restrict a claim by a dual national against its State of nationality.
South America’s Response to the Venezuelan Exodus: A Spirit of Regional Cooperation?
Authors: Ochoa Javier 
Published: November 2020

Abstract
Based on the premise that massive influxes of Venezuelans might overwhelm their asylum systems, South American host States have resorted to ‘Temporary Protection or Stay Arrangements’ (TPSAs) as an uncoordinated but pragmatic response in times of regional hardship. As the Venezuelan situation deteriorated, however, a May 2019 United Nations High Commissioner for Refugees (UNHCR) Guidance Note encouraged host States to apply their extended refugee definitions in tandem with prima facie refugee status determination (PFRSD), an expedited procedure that can prevent the overburdening of asylum capacities. Despite the availability of a more favourable approach, host States have continued to rely on TPSAs, raising questions about whether they truly intend to adopt a regionally coordinated plan, as agreed in the Quito Process. Drawing primarily on domestic refugee legislation and UNHCR’s ‘Guidelines on International Protection No 11’, the article argues that host States’ motivation to provide temporary protection is not so much related to the potential overburdening of their asylum systems but rather to the long-term commitments that would come with the granting of refugee status. It is shown that PFRSD is already regulated in the national laws of four South American States, with the potential of turning into a regional centralized response, but its application remains largely ignored. The article ultimately serves as a reminder for South American governments that displaced Venezuelans do not need temporary humanitarian visas as they are, first and foremost, entitled to legal protection under domestic refugee law.
Factors associated with nurse well-being in relation to electronic health record use: A systematic review
Authors: Nguyen Oliver T , Shah Shivani , Gartland Alexander J , Parekh Arpan , Turner Kea , Feldman Sue S , Merlo Lisa J 
Published: November 2020

Abstract

Objective
Although nurses comprise the largest group of health professionals and electronic health record (EHR) user base, it is unclear how EHR use has affected nurse well-being. This systematic review assesses the multivariable (ie, organizational, nurse, and health information technology [IT]) factors associated with EHR-related nurse well-being and identifies potential improvements recommended by frontline nurses.

Materials and Methods
We searched MEDLINE, Embase, CINAHL, PsycINFO, ProQuest, and Web of Science for literature reporting on EHR use, nurses, and well-being. A quality appraisal was conducted using a previously developed tool.

Results
Of 4583 articles, 12 met inclusion criteria. Two-thirds of the studies were deemed to have a moderate or low risk of bias. Overall, the studies primarily focused on nurse- and IT-level factors, with 1 study examining organizational characteristics. That study found worse nurse well-being was associated with EHRs compared with paper charts. Studies on nurse-level factors suggest that personal digital literacy is one modifiable factor to improving well-being. Additionally, EHRs with integrated displays were associated with improved well-being. Recommendations for improving EHRs suggested IT-, organization-, and policy-level solutions to address the complex nature of EHR-related nurse well-being.

Conclusions
The overarching finding from this synthesis reveals a critical need for multifaceted interventions that better organize, manage, and display information for clinicians to facilitate decision making. Our study also suggests that nurses have valuable insight into ways to reduce EHR-related burden. Future research is needed to test multicomponent interventions that address these complex factors and use participatory approaches to engage nurses in intervention development.
Novel insights into host receptors and receptor-mediated signaling that regulate arbuscular mycorrhizal symbiosis
Authors: Nasir Fahad , Bahadur Ali , Lin Xiaolong , Gao Yingzhi , Tian Chunjie 
Published: November 2020

Abstract
More than 80% of land plant species benefit from symbiotic partnerships with arbuscular mycorrhizal (AM) fungi, which assist in nutrient acquisition and enhance the ability of host plants to adapt to environmental constraints. Host-generated plasma membrane-residing receptor-like kinases and the intracellular α/β-hydrolase DWARF14-LIKE, a putative karrikin receptor, detect the presence of AM fungi before physical contact between the host and fungus. Detection induces appropriate symbiotic responses, which subsequently enables a favorable environment for AM symbiosis to occur. To prevent hyper-colonization and maintain a mutually beneficial association, the host plant precisely monitors and controls AM colonization by receptor-like kinases, such as SUPER NUMERIC NODULES. Previous studies have elucidated how host plant receptors and receptor-mediated signaling regulate AM symbiosis, but the underlying molecular mechanisms remain poorly understood. The identification of a rice CHITIN ELICITOR RECEPTOR KINASE 1 interaction partner, MYC FACTOR RECEPTOR 1, and new insights into DWARF14-LIKE receptor- and SUPER NUMERIC NODULES receptor-mediated signaling have expanded our understanding of how host plant receptors and their corresponding signals regulate AM symbiosis. This review summarizes these and other recent relevant findings. The identified receptors and/or their signaling components could be manipulated to engineer crops with improved agronomic traits by conferring the ability to precisely control AM colonization.
Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites
Authors: Long Pengpeng , Zhang Lu , Huang Bin , Chen Quan , Liu Haiyan 
Published: November 2020

Abstract
We report an approach to predict DNA specificity of the tetracycline repressor (TetR) family transcription regulators (TFRs). First, a genome sequence-based method was streamlined with quantitative P-values defined to filter out reliable predictions. Then, a framework was introduced to incorporate structural data and to train a statistical energy function to score the pairing between TFR and TFR binding site (TFBS) based on sequences. The predictions benchmarked against experiments, TFBSs for 29 out of 30 TFRs were correctly predicted by either the genome sequence-based or the statistical energy-based method. Using P-values or Z-scores as indicators, we estimate that 59.6% of TFRs are covered with relatively reliable predictions by at least one of the two methods, while only 28.7% are covered by the genome sequence-based method alone. Our approach predicts a large number of new TFBs which cannot be correctly retrieved from public databases such as FootprintDB. High-throughput experimental assays suggest that the statistical energy can model the TFBSs of a significant number of TFRs reliably. Thus the energy function may be applied to explore for new TFBSs in respective genomes. It is possible to extend our approach to other transcriptional factor families with sufficient structural information.
A topologically distinct class of photolyases specific for UV lesions within single-stranded DNA
Authors: Emmerich Hans-Joachim , Saft Martin , Schneider Leonie , Kock Dennis , Batschauer Alfred , Essen Lars-Oliver 
Published: November 2020

AbstractPhotolyases are ubiquitously occurring flavoproteins for catalyzing photo repair of UV-induced DNA damages. All photolyases described so far have a bilobal architecture with a C-terminal domain comprising flavin adenine dinucleotide (FAD) as catalytic cofactor and an N-terminal domain capable of harboring an additional antenna chromophore. Using sequence-similarity network analysis we discovered a novel subgroup of the photolyase/cryptochrome superfamily (PCSf), the NewPHLs. NewPHL occur in bacteria and have an inverted topology with an N-terminal catalytic domain and a C-terminal domain for sealing the FAD binding site from solvent access. By characterizing two NewPHL we show a photochemistry characteristic of other PCSf members as well as light-dependent repair of CPD lesions. Given their common specificity towards single-stranded DNA many bacterial species use NewPHL as a substitute for DASH-type photolyases. Given their simplified architecture and function we suggest that NewPHL are close to the evolutionary origin of the PCSf.
Swc4 positively regulates telomere length independently of its roles in NuA4 and SWR1 complexes
Authors: Liu Jia-Cheng , Li Qian-Jin , He Ming-Hong , Hu Can , Dai Pengfei , Meng Fei-Long , Zhou Bo O , Zhou Jin-Qiu 
Published: November 2020

AbstractTelomeres at the ends of eukaryotic chromosomes are essential for genome integrality and stability. In order to identify genes that sustain telomere maintenance independently of telomerase recruitment, we have exploited the phenotype of over-long telomeres in the cells that express Cdc13-Est2 fusion protein, and examined 195 strains, in which individual non-essential gene deletion causes telomere shortening. We have identified 24 genes whose deletion results in dramatic failure of Cdc13-Est2 function, including those encoding components of telomerase, Yku, KEOPS and NMD complexes, as well as quite a few whose functions are not obvious in telomerase activity regulation. We have characterized Swc4, a shared subunit of histone acetyltransferase NuA4 and chromatin remodeling SWR1 (SWR1-C) complexes, in telomere length regulation. Deletion of SWC4, but not other non-essential subunits of either NuA4 or SWR1-C, causes significant telomere shortening. Consistently, simultaneous disassembly of NuA4 and SWR1-C does not affect telomere length. Interestingly, inactivation of Swc4 in telomerase null cells accelerates both telomere shortening and senescence rates. Swc4 associates with telomeric DNA in vivo, suggesting a direct role of Swc4 at telomeres. Taken together, our work reveals a distinct role of Swc4 in telomere length regulation, separable from its canonical roles in both NuA4 and SWR1-C.
The Evans Synthesis of (–)-Nakadomarin A
Authors: Taber Douglass F. 
Published: November 2020

(–)-Nakadomarin A (4), isolated from the marine sponge Amphimedon sp. off the coast of Okinawa, shows interesting cytotoxic and antibacterial activity. David A. Evans of Harvard University prepared (J. Am. Chem. Soc. 2013, 135, 9338) 4 by coupling the enantiomerically pure lactam 2 with the prochiral lactam 1. The preparation of 1 began with the aldehyde 5. Following the Comins protocol, addition of lithio morpholine to the carbonyl gave an intermediate that could be metalated and iodinated. Protection of the aldehyde followed by Heck coupling with allyl alcohol gave the aldehyde 7. Addition of the phosphorane derived from 8 followed by deprotection gave 9 with the expected Z selectivity. Addition of the phosphonate 10 was also Z selective, leading to the lactam 1. The preparation of 2 began with the enantiomerically pure imine 12. The addition of 13 was highly diastereoselective, setting the absolute configuration of 15. Alkylation with the iodide 16 delivered 17, which was closed to 2 under conditions of kinetic ring-closing metathesis, using the Grubbs first generation Ru catalyst. The condensation of 1 with 2 gave both of the diastereomeric products, with a 9:1 preference for the desired 3. Experimentally, acid catalysis alone did not effect cyclization, suggesting that the cyclization is proceeding via silylated intermediates. The diastereoselectivity can be rationalized by a preferred extended transition state for the intramolecular Michael addition. Selective activation of 3 followed by reduction gave 18, which underwent Bischler-Napieralski cyclization to give an intermediate that could be reduced to (–)-nakadomarin A (4). It was later found that exposure of 3 to Tf2O and 19 followed by the addition of Redal gave direct conversion to 4. It is instructive to compare this work to the two previous syntheses of 4 that we have highlighted, by Dixon (OHL May 3, 2010) and by Funk (OHL July 4, 2011). Together, these three independent approaches to 4 showcase the variety and dexterity of current organic synthesis.