bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19-related coagulopathy – Is transferrin a missing link?
Authors: McLaughlin Katie-May , Bechtel Marco , Bojkova Denisa , Wass Mark N. , Michaelis Martin , Cinatl Jindrich 
Published: June 2020

AbstractSARS-CoV-2 is the causative agent of COVID-19. Severe COVID-19 disease has been associated with disseminated intravascular coagulation and thrombosis, but the mechanisms underlying COVID-19-related coagulopathy remain unknown. Since the risk of severe COVID-19 disease is higher in males than in females and increases with age, we combined proteomics data from SARS-CoV-2-infected cells with human gene expression data from the Genotype-Tissue Expression (GTEx) database to identify gene products involved in coagulation that change with age, differ in their levels between females and males, and are regulated in response to SARS-CoV-2 infection. This resulted in the identification of transferrin as a candidate coagulation promoter, whose levels increases with age and are higher in males than in females and that is increased upon SARS-CoV-2 infection. A systematic investigation of gene products associated with the GO term “blood coagulation” did not reveal further high confidence candidates, which are likely to contribute to COVID-19-related coagulopathy. In conclusion, the role of transferrin should be considered in the course of COVID-19 disease and further examined in ongoing clinic-pathological investigations.
Asymptomatic and presymptomatic transmission of SARS-CoV-2: A systematic review
Authors: Savvides Christina , Siegel Robert 
Published: June 2020

AbstractBackground and PurposeMany of the statutes comprising the shelter-in-place and phased-reopening orders are centered around minimizing asymptomatic and presymptomatic transmission. Assumptions about the presence and relative importance of asymptomatic and presymptomatic transmission are based on case reports, the failing of quarantine measures aimed at sequestering ill patients, viral dynamic studies suggesting SARS-CoV-2 production peaks before symptoms appear, and modeling evidence that calculates serial interval between successive generations of infection. In aggregate, these data offer compelling evidence of asymptomatic and presymptomatic transmission, but individually these studies have notable shortcomings that undermine their conclusions. The purpose of this review is to discuss the literature of asymptomatic and presymptomatic transmission, highlight limitations of recent studies, and propose experiments that, if conducted, would provide a more definitive analysis of the relative role of asymptomatic and presymptomatic transmission in the ongoing SARS-CoV-2 pandemic.MethodsWe conducted a systematic review of literature on PubMed using search filters that relate to asymptomatic and presymptomatic transmission as well as serial interval and viral dynamics. We focused on studies that provided primary clinical data.Results34 studies were eligible for inclusion in this systematic review: 11 case reports pertaining to asymptomatic transmission, 9 viral kinetic studies, 13 serial interval studies, and 1 study with viral kinetics and serial interval.ConclusionDifferent approaches to determining the presence and prevalence of asymptomatic and presymptomatic SARS-CoV-2 transmission have notable shortcomings, which were highlighted in this review and limit our ability to draw definitive conclusions. Conducting high quality studies with the aim of understanding the relative role of asymptomatic and presymptomatic transmission is instrumental to developing the most informed policies on reopening our cities, states, and countries.
Reducing SARS-CoV-2 infectious spreading patterns by removing S and R compartments from SIR model equation
Authors: Telles Charles Roberto 
Published: June 2020

AbstractThis research points to the asymptotic instability of SIR model and its variants to predict the behavior of SARS-CoV-2 infection spreading patterns over the population and time aspects. Mainly for the “S” and “R” terms of the equation, the predictive results fail due to confounding environment of variables that sustain the virus contagion within population complex network basis of analysis. While “S” and “R” are not homologous data of analysis, thus with improper topological metrics used in many researches, these terms leads to the asymptotic feature of “I” term as the most stable point of analysis to achieve proper predictive methods. Having in its basis of formulation the policies adopted by countries, “I” therefore presents a stable fixed point orientation in order to be used as a predictive analysis of nearby future patterns of SARS-CoV-2 infection. New metrics using a Weinbull approach for “I” are presented and fixed point orientation (sensitivity of the method) are demonstrated empirically by worldwide statistical data.
Catch and kill airborne SARS-CoV-2 to control spread of COVID-19 by a heated air disinfection system
Authors: Yu Luo , Peel Garrett K. , Cheema Faisal H. , Lawrence William S. , Bukreyeva Natalya , Jinks Christopher W. , Peel Jennifer E. , Peterson Johnny W. , Paessler Slobodan , Hourani Monzer , Ren Zhifeng 
Published: June 2020

AbstractAirborne transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)viaair-conditioning systems poses a significant threat for the continued escalation of the current coronavirus disease (COVID-19) pandemic. Considering that SARS-CoV-2 cannot tolerate temperatures above 70 °C, here we designed and fabricated efficient air disinfection systems based on heated nickel (Ni) foam to catch and kill SARS-CoV-2. Virus test results revealed that 99.8% of the aerosolized SARS-CoV-2 was caught and killed by a single pass through a Ni-foam-based filter when heated up to 200 °C. Additionally, the same filter was also used to catch and kill 99.9% ofBacillus anthracis, an airborne spore. This study paves the way for preventing transmission of SARS-CoV-2 and other highly infectious airborne agents in closed environments.One Sentence SummaryHeated Ni-foam filters are capable of effectively catching and killing airborne SARS-CoV-2 andBacillus anthracisspores.
AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES ANDACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE
Authors: Bickler Stephen W. , Cauvi David M. , Fisch Kathleen M. , Prieto James M. , Gaidry Alicia D. , Thangarajah Hariharan , Lazar David , Ignacio Romeo , Gerstmann Dale R. , Ryan Allen F. , Bickler Philip E. , De Maio Antonio 
Published: June 2020

AbstractOlder aged adults and those with pre-existing conditions are at highest risk for severe COVID-19 associated outcomes. Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts (GSE113957) we investigated whether age affects the expression of pattern recognition receptor (PRR) genes andACE2, the receptor for SARS-CoV-2. Older age was associated with increased expression of PRR genes,ACE2and four genes that encode proteins that have been shown to interact with SAR2-CoV-2 proteins. Assessment of PRR expression might provide a strategy for stratifying the risk of severe COVID-19 disease at both the individual and population levels.
Constitutive overexpression of RAM1 increases arbuscule density during arbuscular mycorrhizal symbiosis in Brachypodium distachyon
Authors: Müller Lena M. , Campos-Soriano Lidia , Levesque-Tremblay Veronique , Bravo Armando , Daniels Dierdra A. , Pathak Sunita , Park Hee-Jin , Harrison Maria J. 
Published: June 2020

AbstractArbuscular mycorrhizal (AM) symbiosis is a mutually beneficial association of plants and fungi of the sub-phylum Glomeromycotina. The endosymbiotic AM fungi colonize the inner cortical cells of the roots, where they form branched hyphae called arbuscules that function in nutrient exchange with the plant. To support arbuscule development and subsequently bidirectional nutrient exchange, the root cortical cells undergo substantial transcriptional re-programming.REDUCED ARBUSCULAR MYCORRHIZA 1 (RAM1), studied in several dicot plant species, is a major regulator of this cortical cell transcriptional program. Here, we generatedram1mutants andRAM1overexpressors in a monocot,Brachypodium distachyon. The AM phenotypes of tworam1linesrevealed thatRAM1is only partly required to enable arbuscule development inB. distachyon. Transgenic lines constitutively overexpressingBdRAM1showed constitutive expression of AM-inducible genes even in the shoots. Following inoculation with AM fungi,BdRAM1-overexpressing roots showed higher arbuscule densities relative to controls, indicating the potential to manipulate the relative proportion of symbiotic interfaces via modulation ofRAM1. However, the overexpressors also show altered expression of hormone biosynthesis genes and aberrant growth patterns including stunted bushy shoots and poor seed set. While these phenotypes possibly provide additional clues aboutBdRAM1’s scope of influence, they also indicate that directed approaches to increase the density of symbiotic interfaces will require a more focused, potentially cell-type specific manipulation of transcription factor gene expression.
Virus survival in evaporated saliva microdroplets deposited on inanimate surfaces
Authors: Fedorenko Aliza , Grinberg Maor , Orevi Tomer , Kashtan Nadav 
Published: June 2020

AbstractThe novel coronavirus respiratory syndrome (COVID-19) has now spread worldwide. The relative contribution of viral transmission via fomites is still unclear. SARS-CoV-2 has been shown to survive on inanimate surfaces for several days, yet the factors that determine its survival on surfaces are not well understood. Here we combine microscopy imaging with virus viability assays to study survival of three bacteriophages suggested as good models for human respiratory pathogens: the enveloped Phi6 (a surrogate for SARS-CoV-2), and the non-enveloped PhiX174 and MS2. We measured virus viability in human saliva microdroplets, SM buffer, and water following deposition on glass surfaces at various relative humidities (RH). Although saliva microdroplets dried out rapidly at all tested RH levels (unlike SM that remained hydrated at RH ≥ 57%), survival of all three viruses in dry saliva microdroplets was significantly higher than in water or SM. Thus, RH and hydration conditions are not sufficient to explain virus survival, indicating that the suspended medium, and association with saliva components in particular, likely affect physicochemical properties that determine virus survival. The observed high virus survival in dry saliva deposited on surfaces, under a wide range of RH levels, can have profound implications for human public health, specifically the COVID-19 pandemic.
Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp
Authors: Eskier Doğa , Suner Aslı , Karakülah Gökhan , Oktay Yavuz 
Published: June 2020

AbstractSince its emergence in Wuhan, China in late 2019, the origin and evolution of SARS-CoV-2 have been among the most debated issues related to COVID-19. Throughout its spread around the world, the viral genome continued acquiring new mutations and some of them became widespread. Among them, 14408 C>T and 23403 A>G mutations in RdRp and S, respectively, became dominant in Europe and the US, which led to debates regarding their effects on the mutability and transmissibility of the virus. In this study, we aimed to investigate possible differences between time-dependent variation of mutation densities (MDe) of viral strains that carry these two mutations and those that do not. Our analyses at the genome and gene level led to two important findings: First, time-dependent changes in the average MDe of circulating SARS-CoV-2 genomes showed different characteristics before and after the beginning of April, when daily new case numbers started levelling off. Second, this pattern was much delayed or even non-existent for the “mutant” (MT) strain that harbored both 14408 C>T and 23403 A>G mutations. Although these differences were not limited to a few hotspots, it is intriguing that the MDe increase is most evident in two critical genes, S and Orf1ab, which are also the genes that harbor the defining mutations of the MT genotype. The nature of these unexpected relationships warrant further research.
The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection
Authors: Beddingfield Brandon , Iwanaga Naoki , Chapagain Prem , Zheng Wenshu , Roy Chad J. , Hu Tony Y. , Kolls Jay , Bix Gregory 
Published: June 2020

SUMMARYMany efforts to design and screen therapeutics for severe acute respiratory syndrome coronavirus (SARS-CoV-2) have focused on inhibiting viral cell entry by disrupting ACE2 binding with the SARS-CoV-2 spike protein. This work focuses on inhibiting SARS-CoV-2 entry through a hypothesized α5β1 integrin-based mechanism, and indicates that inhibiting the spike protein interaction with α5β1 integrin (+/− ACE2), and the interaction between α5β1 integrin and ACE2 using a molecule ATN-161 represents a promising approach to treat COVID-19.
Fatty acid composition and parasitism of European sardine (Sardina pilchardus) and European anchovy (Engraulis encrasicolus) populations in the northern Catalan Sea in the context of changing environmental conditions
Authors: Biton-Porsmoguer Sebastian , Bou Ricard , Lloret Elsa , Alcaide Manuel , Lloret Josep 
Published: June 2020

AbstractThe status of sardine and anchovy populations in the northern Mediterranean Sea has been declining in recent decades. In this study, fatty acids and parasitism at different reproductive and feeding stages in these two species were assessed using specimens caught along the northern Catalan coast, in order to assess the links between lipid dynamics, reproduction and feeding in these two species, and to contribute towards an explanation of the potential causes of the current situation of the stocks. The results support the use of fatty acid levels as indicators of the body condition of sardine and anchovy at different reproductive and feeding stages, as well as that of the pelagic environmental conditions. In particular, the relatively low n-3 PUFA levels (which are crucial for reproductive success) found in spawning sardines compared to spawning anchovies indicate a poorer reproductive health status of sardine. By comparing the current total lipid content values with those recorded in other Mediterranean and North Atlantic areas, and, others from more than ten years ago, in the adjacent area of the Gulf of Lion, our study reveals the persistent poor condition of sardine and anchovy in the northern Catalan Sea. Furthermore, the low levels of diatom fatty acid markers observed throughout the spawning and non-spawning seasons in both sardine and anchovy, indicate a diet poor in diatoms. Moreover, the results indicate that it is very unlikely that parasitism is a significant factor in the decline in condition of sardine and anchovy in the northern Catalan Sea. In fact, the results suggest that the current poor condition of sardine and anchovy in the northern Catalan Sea has been exacerbated by a decrease in plankton productivity and/or a shift in the taxonomic composition of phytoplankton communities, adding to the ongoing effects of overfishing.
Cascade of care, awareness and treatment of Chronic Hepatitis B in Malaysia- findings from a community-based screening campaign
Authors: Lim ZZ , Teo JS , Tan AC , Siam Tan Soek , Mohamed Rosmawati , Goh KL , Lee YY , Lai WH , Lim TO 
Published: June 2020

SummaryIntroductionIn 2016 the World Health Organization (WHO) had adopted a global strategy to eliminate Hepatitis B (HBV) by 2030 through five core interventions, the first four were preventive while the fifth is the “cascade of care”, the continuum of services that persons with chronic HBV should receive as they progress from screening to diagnosis to treatment to chronic care. We determined the prevalence of the awareness and treatment of chronic HBV in Malaysia based on a large sample data from a screening campaign.MethodsA total of 10,436 subjects participated in the HBV screening campaign organized by the Hepatitis Free Pahang Malaysia (HFPM) in 2018 and 2019. All screen-positive subjects were recalled to undergo laboratory-based HBsAg and HBV DNA tests. Patients with confirmed chronic HBV were referred to local health services, while continued being monitored by HFPM.ResultsWe estimated 13.1% of Malaysian adults aged 20 or older with chronic HBV were aware of their HBV status, and of those only 0.7% had received prior anti-viral treatment, but among those with baseline HBV DNA level>20,000 IU/ml, 15.6% were subsequently treated. Tenofovir disoproxil fumarate was the only medicine used on all treated patients. The linkage to care post-screening was broken in substantial number of patients, only 108 (54%) subjects had returned to have their HBV DNA measured and only 115 (58%) patients had subsequently sought care and were on still follow-up.ConclusionFew Malaysian adults with HBV were aware of their infection and even less received anti-viral therapy. Concerted public health efforts are urgently needed to improve HBV screening and care cascade in order to meet WHO’s targets for HBV elimination.
Automatic phenotyping of electronical health record: PheVis algorithm
Authors: Ferté Thomas , Cossin Sébastien , Schaeverbeke Thierry , Barnetche Thomas , Jouhet Vianney , Hejblum Boris P 
Published: June 2020

AbstractElectronic Health Records (EHRs) often lack reliable annotation of patient medical conditions. Yu et al. recently proposed PheNorm, an automated unsupervised algorithm to identify patient medical conditions from EHR data. PheVis extends PheNorm at the visit resolution. PheVis combines diagnosis codes together with medical concepts extracted from medical notes, incorporating past history in a machine learning approach to provide an interpretable “white box” predictor of the occurrence probability for a given medical condition at each visit. PheVis is applied to two real-world use-cases using the datawarehouse of the University Hospital of Bordeaux: i) rheumatoid arthritis, a chronic condition; ii) tuberculosis, an acute condition (cross-validated AUROC were respectively 0.947 [0.944; 0.948] and 0.987 [0.983; 0.990]). PheVis performs well for chronic conditions, though absence of exclusion of past medical history by natural language processing tools limits its performance in French for acute conditions. It achieves significantly better performance than state-of-the-art methods especially for chronic diseases.
The effect of serological screening for SARS-CoV-2 antibodies to participants’ attitudes and risk behaviour: a study on a tested population sample of industry workers in Split-Dalmatia County, Croatia
Authors: Ljubić Toni , Banovac Ana , Buljan Ivan , Jerković Ivan , Bašić Željana , Kružić Ivana , Kolić Andrea , Kolombatović Rino Rivi , Marušić Ana , Anđelinović Šimun 
Published: June 2020

ABSTRACTRapid serological tests for SARS-CoV-2 antibodies have been questioned by scientists and the public because of unexplored effects of negative test results on behaviour and attitudes, that could lower the level of adherence to protective measures. Therefore, our study aimed to investigate the changes in personal attitudes and behaviour before and after negative serological test results for SARS-CoV-2 antibodies. We conducted a survey questionnaire on 200 industry workers (69% males and 31% females) that have been previously tested negative. The survey examined participants’ self-reported general attitudes towards COVID-19, sense of fear, as well as their behaviour related to protective measures before and after the testing. The participants perceived the disease as a severe health threat and acknowledged the protective measures as appropriate. They reported a high level of adherence to measures and low level of fear both before and after the testing. Although those indicators were statistically significantly reduced after the test (P < 0.004), they did not result in risk behaviour. Therefore, the serological tests are not an additional threat regarding the risk behaviour in an environment where protective measures are efficient. In contrast, they might contribute to reducing the fear in the society and working environment.
Causes of Death and Comorbidities in Patients with COVID-19
Authors: Elezkurtaj Sefer , Greuel Selina , Ihlow Jana , Michaelis Edward , Bischoff Philip , Kunze Catarina Alisa , Sinn Bruno Valentin , Gerhold Manuela , Hauptmann Kathrin , Ingold-Heppner Barbara , Miller Florian , Herbst Hermann , Corman Victor Max , Martin Hubert , Radbruch Helena , Heppner Frank L. , Horst David 
Published: June 2020

ABSTRACTInfection by the new corona virus strain SARS-CoV-2 and its related syndrome COVID-19 has caused several hundreds of thousands of deaths worldwide. Patients of higher age and with preexisting chronic health conditions are at an increased risk of fatal disease outcome. However, detailed information on causes of death and the contribution of comorbidities to death yet is missing. Here, we report autopsy findings on causes of death and comorbidities of 26 decedents that had clinically presented with severe COVID-19. We found that septic shock and multi organ failure was the most common immediate cause of death, often due to suppurative pulmonary infection. Respiratory failure due to diffuse alveolar damage presented as the most immediate cause of death in fewer cases. Several comorbidities, such as hypertension, ischemic heart disease, and obesity were present in the vast majority of patients. Our findings reveal that causes of death were directly related to COVID-19 in the majority of decedents, while they appear not to be an immediate result of preexisting health conditions and comorbidities. We therefore suggest that the majority of patients had died of COVID-19 with only contributory implications of preexisting health conditions to the mechanism of death.
Diagnostic accuracy of six commercial SARS-CoV-2 IgG/total antibody assays and identification of SARS-CoV-2 neutralizing antibodies in convalescent sera
Authors: Strömer Annabelle , Grobe Olaf , Rose Ruben , Fickenscher Helmut , Lorentz Thomas , Krumbholz Andi 
Published: June 2020

AbstractThe reliable detection of immunoglobulin G (IgG) or total antibodies directed against the novel severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is important for clinical diagnostics and epidemiological studies.Here, we compare the diagnostic accuracy of six commercially available SARS-CoV-2 IgG (Abbott SARS-CoV-2 IgG; Diasorin Liaison® SARS-CoV-2 S1/2 IgG; Epitope EDI™ Novel Coronavirus COVID-19 IgG ELISA Kit; Euroimmun Anti-SARS-CoV-2 ELISA (IgG); Mikrogen recomWell SARS-CoV-2 IgG) or total SARS-CoV-2 antibody assays (Roche Elecsys Anti-SARS-CoV-2).The test sensitivities were analyzed with a set of 34 sera obtained from 26 patients after PCR-confirmed SARS-CoV-2 infection and varied from 76.9% (Euroimmun) to 96.2% (Abbott). The majority of assay results were confirmed in a laboratory-developed plaque reduction neutralization test and by a SARS-CoV-2 IgG-specific line assay including measurement of generally low IgG avidities (Mikrogen recomLine Coronavirus IgG [Avidität], prototype).Moreover, 100 stored sera collected during summer 2018 (N = 50) and winter season 2018/2019 (N = 50) were included to demonstrate test specificities. These varied from 96.0% (DiaSorin) to 100% (Epitope EDI™).A subset of sera were retested with a lateral flow test (STANDARD Q COVID-19 IgM/IgG Duo) and a considerably lower sensitivity was noted.Overall, the diagnostic accuracy of the six SARS-CoV-2 IgG/total antibody assays was good and varied from 92.9% (Euroimmun) to 98.4% (Abbott). Due to the different specificities, results of commercially available SARS-CoV-2 antibody tests should be interpreted with caution. A high proportion of antibody-positive patient sera demonstrated neutralizing capacity against SARS-CoV-2.