bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining antibody markers for serosurveillance of SARS-CoV-2 to estimate seroprevalence and time-since-infection
Authors: Bhuiyan Md S. , Brintz Ben J. , Whitcombe Alana L. , Markmann Alena J. , Bartelt Luther A. , Moreland Nicole J. , Azman Andrew S. , Leung Daniel T. 
Published: January 2022

Abstract
Serosurveillance is an important epidemiologic tool for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), used to estimate infection rates and the degree of population immunity. There is no general agreement on which antibody biomarker(s) should be used, especially with the rollout of vaccines globally. Here, we used random forest models to demonstrate that a single spike or receptor-binding domain (RBD) antibody was adequate for classifying prior infection, while a combination of two antibody biomarkers performed better than any single marker for estimating time-since-infection. Nucleocapsid antibodies performed worse than spike or RBD antibodies for classification, but can be useful for estimating time-since-infection, and in distinguishing infection-induced from vaccine-induced responses. Our analysis has the potential to inform the design of serosurveys for SARS-CoV-2, including decisions regarding a number of antibody biomarkers measured.
Characteristics of transmission routes of COVID-19 cluster infections in Gangwon Province, Korea
Authors: Lim Chaeyun , Nam Youngju , Oh Won Sup , Ham Sugeun , Kim Eunmi , Kim Myeonggi , Kim Saerom , Kim Yeojin , Jeong Seungmin 
Published: January 2022

Abstract
This study investigated the characteristics of transmission routes of COVID-19 cluster infections (⩾10 linked cases within a short period) in Gangwon Province between 22 February 2020 and 31 May 2021. Transmission routes were divided into five major categories and 35 sub-categories according to the relationship between the infector and the infectee and the location of transmission. A total of 61 clusters occurred during the study period, including 1741 confirmed cases (55.7% of all confirmed cases (n = 3125)). The the five major routes of transmission were as follows: ‘using (staying in) the same facility (50.7%), ‘cohabiting family members’ (23.3%), ‘social gatherings with acquaintances’ (10.8%), ‘other transmission routes’ (7.0%), and ‘social gatherings with non-cohabiting family members/relatives’ (5.5%). For transmission caused by using (staying in) the same facility, the highest number of confirmed cases was associated with churches, followed by medical institutions (inpatient), sports facilities, military bases, offices, nightlife businesses, schools, restaurants, day-care centres and kindergarten, and service businesses. Our analysis highlights specific locations with frequent transmission of infections, and transmission routes that should be targeted in situations where adherence to disease control rules is difficult.
Whole-genome sequencing of Mycobacterium tuberculosis for prediction of drug resistance
Authors: Wang Luqi , Yang Jinghui , Chen Liang , Wang Weibing , Yu Fangyou , Xiong Haiyan 
Published: January 2022

Abstract
Whole-genome sequencing (WGS) has shown tremendous potential in rapid diagnosis of drug-resistant tuberculosis (TB). In the current study, we performed WGS on drug-resistant Mycobacterium tuberculosis isolates obtained from Shanghai (n = 137) and Russia (n = 78). We aimed to characterise the underlying and high-frequency novel drug-resistance-conferring mutations, and also create valuable combinations of resistance mutations with high predictive sensitivity to predict multidrug- and extensively drug-resistant tuberculosis (MDR/XDR-TB) phenotype using a bootstrap method. Most strains belonged to L2.2, L4.2, L4.4, L4.5 and L4.8 lineages. We found that WGS could predict 82.07% of phenotypically drug-resistant domestic strains. The prediction sensitivity for rifampicin (RIF), isoniazid (INH), ethambutol (EMB), streptomycin (STR), ofloxacin (OFL), amikacin (AMK) and capreomycin (CAP) was 79.71%, 86.30%, 76.47%, 88.37%, 83.33%, 70.00% and 70.00%, respectively. The mutation combination with the highest sensitivity for MDR prediction was rpoB S450L + rpoB H445A/P + katG S315T + inhA I21T + inhA S94A, with a sensitivity of 92.17% (0.8615, 0.9646), and the mutation combination with highest sensitivity for XDR prediction was rpoB S450L + katG S315T + gyrA D94G + rrs A1401G, with a sensitivity of 92.86% (0.8158, 0.9796). The molecular information presented here will be of particular value for the rapid clinical detection of MDR- and XDR-TB isolates through laboratory diagnosis.
Viticulture, opus doliare, and the patrimonium Caesaris at the Roman imperial estate at Vagnari (Puglia)
Authors: Carroll Maureen 
Published: January 2022

AbstractThis article focuses on the establishment of a winery on the Roman imperial estate at Vagnari in southeast Italy in the 2nd c. CE and the ceramic vats (dolia defossa) needed to mature and store the estate's vintages. A scientific analysis of the clay used to make the dolia has revealed their likely place of manufacture to have been in Latium or on the border between Latium and Campania on the Tyrrhenian (west) coast of Italy. With these analytical results in hand, it is now possible to inquire into the historical and economic significance for the imperial fiscus of importing dolia for wine making in the vicus at Vagnari, the route and mechanisms by which they might have traveled to the other side of the Italian peninsula, and the connectivity between this Apulian imperial estate and other potential imperial properties in western Italy. This places the present study at the intersection of agriculture, manufacturing, and property transfer within the patrimonium Caesaris.
Point-of-Care Ultrasound Use by EMS Providers in Out-of-Hospital Cardiac Arrest
Authors: Kreiser Michael A. , Hill Brieanna , Karki Dikchhya , Wood Elke , Shelton Ryan , Peterson Jodi , Riccio John , Zapata Isain , Khalil Paul A. , Gubler Dean , LaPorta Anthony J. , Roosevelt Genie E. , Toney Amanda G. 
Published: January 2022

AbstractAim:Paramedics received training in point-of-care ultrasound (POCUS) to assess for cardiac contractility during management of medical out-of-hospital cardiac arrest (OHCA). The primary outcome was the percentage of adequate POCUS video acquisition and accurate video interpretation during OHCA resuscitations. Secondary outcomes included POCUS impact on patient management and resuscitation protocol adherence.Methods:A prospective, observational cohort study of paramedics was performed following a four-hour training session, which included a didactic lecture and hands-on POCUS instruction. The Prehospital Echocardiogram in Cardiac Arrest (PECA) protocol was developed and integrated into the resuscitation algorithm for medical non-shockable OHCA. The ultrasound (US) images were reviewed by a single POCUS expert investigator to determine the adequacy of the POCUS video acquisition and accuracy of the video interpretation. Change in patient management and resuscitation protocol adherence data, including end-tidal carbon dioxide (EtCO2) monitoring following advanced airway placement, adrenaline administration, and compression pauses under ten seconds, were queried from the prehospital electronic health record (EHR).Results:Captured images were deemed adequate in 42/49 (85.7%) scans and paramedic interpretation of sonography was accurate in 43/49 (87.7%) scans. The POCUS results altered patient management in 14/49 (28.6%) cases. Paramedics adhered to EtCO2 monitoring in 36/36 (100.0%) patients with an advanced airway, adrenaline administration for 38/38 (100.0%) patients, and compression pauses under ten seconds for 36/38 (94.7%) patients.Conclusion:Paramedics were able to accurately obtain and interpret cardiac POCUS videos during medical OHCA while adhering to a resuscitation protocol. These findings suggest that POCUS can be effectively integrated into paramedic protocols for medical OHCA.
Terrorist Attacks in Western Europe: A Counter-Terrorism Medicine Analysis
Authors: Tin Derrick , Barten Dennis G. , De Cauwer Harald , Mortelmans Luc JM , Ciottone Gregory R. 
Published: January 2022

AbstractBackground:The modern concept of terrorism has its roots in the “old continent” of Western Europe, more specifically in France, during the “Reign of Terror” period of the French Revolution. At the time, this form of state terror had a positive connotation: it was a legitimate means of defending the young state. While no single accepted definition of terrorism exists today, it is universally considered an attack on both state and society. The health care impacts of terrorist attacks often extend disproportionally beyond the casualty toll, but the potential for such events to induce mass casualties remains a concern to Disaster Medicine and Counter-Terrorism Medicine (CTM) specialists.Method:Data collection was performed using a retrospective database search through the Global Terrorism Database (GTD). The GTD was searched using the internal database search functions for all events which occurred in Western Europe from January 1, 1970 - December 31, 2019. Years 2020 and 2021 were not yet available at the time of the study. Primary weapon type, country where the incident occurred, and number of deaths and injured were collated. Results were exported into an Excel spreadsheet (Microsoft Corp.; Redmond, Washington USA) for analysis.Results:A total of 15,306 events were recorded in Western Europe out of a total of 201,183 events world-wide between the years 1970 and 2019 inclusive. This resulted in a total of 5,548 deaths and 17,187 injuries. Explosives were used as a primary weapon/attack modality in 8,103 attacks, followed by incendiary attacks in 3,050 events and firearm use in 2,955 events. The use of chemical, biological, radiation, and nuclear (CBRN) weapons was rare and only accounted for 47 events.Conclusion:From 1970 through 2019, 9.11% of all terrorist attacks occurred in Western Europe. Compared to global trends of attack methodologies in the same study period, the use of explosives as a primary attack modality in Western Europe was similar (52.94% in Western Europe versus 48.78% Global). Firearm use was comparatively low (19.31% versus 26.77%) and the use of CBRN as an attack modality was rare (0.30% versus 0.20%). The United Kingdom, Spain, and France accounted for over 65% of all terrorist attacks and over 75% of terrorism-related deaths in Western Europe.
Answering Fuzzy Queries over Fuzzy DL-Lite Ontologies
Authors: PASI GABRIELLA , PEÑALOZA RAFAEL 
Published: January 2022

AbstractA prominent problem in knowledge representation is how to answer queries taking into account also the implicit consequences of an ontology representing domain knowledge. While this problem has been widely studied within the realm of description logic ontologies, it has been surprisingly neglected within the context of vague or imprecise knowledge, particularly from the point of view of mathematical fuzzy logic. In this paper, we study the problem of answering conjunctive queries and threshold queries w.r.t. ontologies in fuzzy DL-Lite. Specifically, we show through a rewriting approach that threshold query answering w.r.t. consistent ontologies remains in
${AC}^{0}$
in data complexity, but that conjunctive query answering is highly dependent on the selected triangular norm, which has an impact on the underlying semantics. For the idempotent Gödel t-norm, we provide an effective method based on a reduction to the classical case.
Assessment of Acacia dealbata as green manure and weed control for maize crop
Authors: Lorenzo Paula , Álvarez-Iglesias Lorena , González Luís , Revilla Pedro 
Published: January 2022

AbstractAcacia dealbata Link is one of the main invasive species in southwestern Europe and a resource with potential value for agriculture. Our objective was to assess the value of A. dealbata vegetative aerial biomass used as green manure and as a tool for weed control in maize crops through three sequential experiments. In 2017, an experiment was carried out with acacia green manure vs inorganic fertilization of pots sown with a field corn and a sweet corn hybrid with strong and weak nutrient demand, respectively. Nutrients were not released from acacia green manure at an appropriate timing, and maize suffered nutrient deficit. In 2018, a pot experiment was made outdoors incorporating acacia green manure at different times before maize sowing, and we found that a 4-month period was required for maximum nutrient release from acacia green manure. In 2019, an early and a late-field experiments were performed by incorporating acacia green manure 4 months before maize sowing. Physiological and agronomic data were recorded in maize, along with soil data, for all years, and weed data the last year. Altogether, most effects and interactions between genotype or environment and fertilization treatment were not significant, and some deficiencies caused by acacia green manure fertilization depend on genotype and environment. Incorporation of acacia green manure 4 months before maize sowing partially controlled weeds and replaced inorganic fertilization. However, deficiencies should be corrected with additional weed control practices and fertilization treatments, according to the nutrient demand of the crop and the soil environment.
Lignin Preservation and Microbial Carbohydrate Metabolism in Permafrost Soils
Authors: Dao Thao Thi , Mikutta Robert , Sauheitl Leopold , Gentsch Norman , Shibistova Olga , Wild Birgit , Schnecker Jörg , Bárta Jiří , Čapek Petr , Gittel Antje , Lashchinskiy Nikolay , Urich Tim , Šantrůčková Hana , Richter Andreas , Guggenberger Georg 
Published: January 2022

AbstractPermafrost‐affected soils in the northern circumpolar region store more than 1,000 Pg soil organic carbon (OC), and are strongly vulnerable to climatic warming. However, the extent to which changing soil environmental conditions with permafrost thaw affects different compounds of soil organic matter (OM) is poorly understood. Here, we assessed the fate of lignin and non‐cellulosic carbohydrates in density fractionated soils (light fraction, LF vs. heavy fraction, HF) from three permafrost regions with decreasing continentality, expanding from east to west of northern Siberia (Cherskiy, Logata, Tazovskiy, respectively). In soils at the Tazovskiy site with thicker active layers, the LF showed smaller OC‐normalized contents of lignin‐derived phenols and plant‐derived sugars and a decrease of these compounds with soil depth, while a constant or even increasing trend was observed in soils with shallower active layers (Cherskiy and Logata). Also in the HF, soils at the Tazovskiy site had smaller contents of OC‐normalized lignin‐derived phenols and plant‐derived sugars along with more pronounced indicators of oxidative lignin decomposition and production of microbial‐derived sugars. Active layer deepening, thus, likely favors the decomposition of lignin and plant‐derived sugars, that is, lignocelluloses, by increasing water drainage and aeration. Our study suggests that climate‐induced degradation of permafrost soils may promote carbon losses from lignin and associated polysaccharides by abolishing context‐specific preservation mechanisms. However, relations of OC‐based lignin‐derived phenols and sugars in the HF with mineralogical properties suggest that future OM transformation and carbon losses will be modulated in addition by reactive soil minerals.
Modeling of Diffuse Auroral Emission at Mars: Contribution of MeV Protons
Authors: Nakamura Yuki , Terada Naoki , Leblanc François , Rahmati Ali , Nakagawa Hiromu , Sakai Shotaro , Hiruba Sayano , Kataoka Ryuho , Murase Kiyoka 
Published: January 2022

AbstractThe Solar Energetic Particle and imaging ultraviolet spectrograph (IUVS) instruments onboard the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft discovered diffuse aurora that span across the nightside of Mars due to the interaction of solar energetic particles (SEPs) with the Martian atmosphere. However, it is unclear whether the diffuse aurora originates from energetic electrons or protons. We have developed a Monte Carlo model to calculate the limb intensity profile of the CO2+ ultraviolet doublet (UVD) due to precipitation of energetic electrons and protons with energy ranges from 100 eV to 100 keV and from 50 keV to 5 MeV, respectively. We used electron and proton fluxes observed by MAVEN during the December 2014 SEP event and the September 2017 SEP event. Our results showed that proton‐induced CO2+ UVD emission has a lower peak altitude than electron‐induced CO2+ UVD emission. The calculated peak altitudes of the CO2+ UVD limb profiles are 76 and 68 km in the December 2014 event and the September 2017 event, respectively. Extending the energy to 500 keV for electrons and 20 MeV for protons further improved our comparison to the IUVS observations. We have succeeded in reproducing peak altitudes and shapes of the observed CO2+ UVD limb profiles using the SEP flux observed by MAVEN. This was possible by taking into account the contribution of energetic protons, indicating that both energetic electrons and protons contribute to producing the observed diffuse aurora.
Relativistic Electron Precipitation Near Midnight: Drivers, Distribution, and Properties
Authors: Capannolo L. , Li W. , Millan R. , Smith D. , Sivadas N. , Sample J. , Shekhar S. 
Published: January 2022

AbstractWe analyze the drivers, distribution, and properties of the relativistic electron precipitation (REP) detected near midnight by the Polar Orbiting Environmental Satellites (POES) and Meteorological Operational (MetOp) satellites, critical for understanding radiation belt losses and nightside atmospheric energy input. REP is either driven by wave‐particle interactions (isolated precipitation within the outer radiation belt), or current sheet scattering (CSS; precipitation with energy dispersion), or a combination of the two. We evaluate the L‐MLT distribution for the identified REP events in which only one process evidently drove the precipitation (∼10% of the REP near midnight). We show that the two mechanisms coexist and drive precipitation in a broad L‐shell range (4–7). However, wave‐driven REP was also observed at L < 4, whereas CSS‐driven REP was also detected at L > 7. Moreover, we estimate the magnetotail stretching during each REP event using the magnetic field observations from the Geostationary Operational Environmental Satellite (GOES). Both wave‐particle interactions and CSS drive REP in association with a stretched magnetotail, although CSS‐driven REP potentially shows more pronounced stretching. Wave‐driven REP events are localized in L shell and often occur on spatial scales of <0.3 L. Using either proton precipitation (observed by POES/MetOp during wave‐driven REP) as a proxy for electromagnetic ion cyclotron (EMIC) wave activity or wave observations (from GOES and the Van Allen Probes) at the conjugate event location, we find that ∼73% wave‐driven REP events are associated with EMIC waves.
Evidence for Deeply Subducted Lower‐Plate Seamounts at the Hikurangi Subduction Margin: Implications for Seismic and Aseismic Behavior
Authors: Chow Bryant , Kaneko Yoshihiro , Townend John 
Published: January 2022

AbstractSeamounts are found at many subduction zones and act as seafloor heterogeneities that affect slip behavior on megathrusts. At the Hikurangi subduction zone offshore the North Island, New Zealand, seamounts have been identified on the incoming Pacific plate and below the accretionary prism, but there is little concrete evidence for seamounts subducted beyond the present‐day coastline. Using a high‐resolution, adjoint tomography‐derived velocity model of the North Island, we identify two high‐velocity anomalies below the East Coast and an intraslab low‐velocity zone up‐dip of one of these anomalies. We interpret the high‐velocity anomalies as previously unidentified, deeply subducted seamounts, and the low‐velocity zone as fluid in the subducting slab. The seamounts are inferred to be 10–30 km wide and on the plate interface at 12–15 km depth. Resolution analysis using point spread functions confirms that these are well‐resolved features. The locations of the two seamounts coincide with bathymetric features whose geometries are consistent with those predicted from analog experiments and numerical simulations of seamount subduction. The spatial characteristics of seismicity and slow slip events near the inferred seamounts agree well with previous numerical modeling predictions of the effects of seamount subduction on megathrust stress and slip. Anomalous geophysical signatures, magnetic anomalies, and swarm seismicity have also been observed previously at one or both seamount locations. We propose that permanent fracturing of the northern Hikurangi upper plate by repeated seamount subduction may be responsible for the dichotomous slow slip behavior observed geodetically, and partly responsible for along‐strike variations in plate coupling on the Hikurangi subduction interface.
Crustal Structure Beneath the Northern Appalachians and the Eastern Grenville Province
Authors: Bagherpur Mojaver Omid , Darbyshire Fiona 
Published: January 2022

AbstractSoutheastern Canada and the northeastern USA include terranes that were tectonized since the Archean, making this region an excellent place to investigate the evolution of continental crust. Our study area covers the Archean southeastern Superior Province, the Proterozoic eastern Grenville, and the Phanerozoic northern Appalachians comprising terranes with either Peri‐Laurentian or Peri‐Gondwanan heritage. Adopting a Rayleigh wave ambient noise tomography method, we used noise data recorded between 2013 and 2015, and obtained high resolution anisotropic tomographic images of the crust enabling us to discuss tectonic implications. The azimuthal anisotropy orientations follow a dominant NE‐SW trend across the study area, but some localized changes of anisotropy direction in the Bay of Fundy and across the Appalachian front are observed. The crust beneath the older Superior and Grenville provinces is generally fast, whereas the Appalachians include strong slow anomalies, especially at upper crustal depths, where they represent thick sedimentary basins beneath the St. Lawrence valley, the Gulf of St. Lawrence, and the Bay of Fundy. We suggest that the boundary between the Peri‐Laurentian and the Peri‐Gondwanan terranes at depth is marked by a Moho‐offset feature observable in our models. A generally similar crustal seismic signature for the two youngest easternmost tectonic domains suggest that they were never separated by a wide ocean basin. Our results provide important evidence for evolution of the continental crust during and after accretionary/collisional episodes in the study area.
Focusing and Defocusing of Tropical Cyclone Generated Waves by Ocean Current Refraction
Authors: Sun Rui , Villas Bôas Ana B. , Subramanian Aneesh C. , Cornuelle Bruce D. , Mazloff Matthew R. , Miller Arthur J. , Langodan Sabique , Hoteit Ibrahim 
Published: January 2022

AbstractWaves generated by tropical cyclones can have devastating effects on coastal regions. However, the role of ocean currents in modifying wave amplitudes, wavelengths, and directions is commonly overlooked in wave forecasts, despite the fact that these interactions can lead to extreme wave conditions. Here, we use satellite observations and wave modeling to quantify the effects of ocean currents on the surface waves generated during a tropical cyclone event in the Arabian Sea. As a case study, this paper documents beams of wave heights originating from the eyewall of a tropical cyclone caused by current‐induced refraction. Alternating regions of high and low wave heights in the model simulations are consistent with observations and extend for thousands of kilometers all the way to 100 m isobath. Our results highlight the importance of accounting for wave refraction by currents in order to accurately predict the impact of tropical cyclone generated waves on coastal regions.