bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 in human sewage in Santa Catalina, Brazil, November 2019
Authors: Fongaro Gislaine , Hermes Stoco Patrícia , Marques Souza Dóris Sobral , Grisard Edmundo Carlos , Magri Maria Elisa , Rogovski Paula , André Schörner Marcos , Barazzetti Fernando Hartmann , Christoff Ana Paula , de Oliveira Luiz Felipe Valter , Bazzo Maria Luiza , Wagner Glauber , Hernández Marta , Rodriguez-Lázaro David 
Published: June 2020

AbstractWe analysed human sewage located in Florianópolis (Santa Catalina, Brazil) from late October until the Brazil lockdown on early March. We detected SARS-CoV-2 in two samples collected independently on 27th November 2019 (5.49±0.02 log genome copies/L). Subsequent samplings were positive until 4th March 2020 (coinciding with the first COVID-19 case reported in Santa Catalina), with a SARS-CoV-2 RNA increase of one log (6.68±0.02 log genome copies/L). Our results show that SARS-CoV-2 has been circulating in Brazil since late November 2019, much earlier than the first reported case in the Americas (21st January 2020, USA).
Combination of Antibody based rapid diagnostic tests used in an algorithm may improve their performance in SARS CoV-2 diagnosis
Authors: Kushemererwa Grace Esther , Kayongo Ismail , Semanda Patrick , Nansumba Hellen , Tadeo Iga , Namulindwa Christine , Nyegenye Wilson , Kiyaga Charles , Ogwok Patrick , Ndidde Susan , Ssewanyana Isaac 
Published: June 2020

AbstractBackgroundGlobally response to the SARS-CoV-2 pandemic is highly limited by diagnostic methods. Currently, World Health Organization (WHO) recommends the use of molecular assays for confirmation of SARS-CoV-2 infection which are highly expensive and require specialized laboratory equipment. This is a limitation in mass testing and in low resource settings. SARS CoV-2 IgG/IgM antibody tests have had poor diagnostic performance that do not guarantee their use in diagnostics. In this study we demonstrate a concept of using a combination of RDTs in an algorithm to improve their performance for diagnostics.MethodEighty six (86) EDTA whole blood samples were collected from SARS-CoV-2 positive cases admitted at Masaka and Mbarara Regional Referral Hospitals in Uganda. These were categorized from day when confirmed positive as follows; category A (0-3 days, 10 samples), category B (4-7 days, 20 samples), Category C (8-17 days, 11 samples) and Category D (18-28 days, 20 samples). Plasma was prepared, transported to the testing laboratory and stored at −200C prior to testing. A total of 13 RDTS were tested following manufacturer’s instructions. Data was entered in Microsoft Excel exported to STATA for computation of sensitivity and specificity. We computed for all possible combinations of 2 of the 13 RDTS (13C2) that were evaluated in parallel algorithm.ResultsThe individual sensitives of the RDTs ranged between 74% and 18% and there was a general increasing trend across the categories with days since PCR confirmation. A total of 78 possible combinations of the RDTs to be used in parallel was computated. The combinations of the 2 RDTS improved the sensitivities to 90%.DiscussionWe demonstrate that use of RDTs in combinations can improve their overall sensitivity. This approach when used on a wider range of combination of RDTs may yield combinations that can give sensitivities that are of diagnostics relevance in mass testing and low resource setting.
Evidence suggests a novel cerebrospinal circulatory system exists in human nerves
Authors: Pessa Joel E 
Published: June 2020

ABSTRACTEvidence from a 5-year study including 150 fresh human cadaver dissections, microsurgery, fluorescent microinjections, immunohistochemistry and confocal imaging suggests a novel CSF circulatory system exists in human nerves. We introduced this system in 2017. Here we provide further evidence to support our conclusion. No previous manuscript, text, or atlas has identified a CSF circulatory system in nerves. The human nervous system is devoid of lymphatics. CSF vessels in human nerves are distinct from blood vessels and lymphatics; may be a remnant of the primitive circulatory system in multi-cellular organisms; and likely predate the vascular circulation in animals.
Facilitating mGluR4 activity reverses the long-term deleterious consequences of chronic morphine exposure
Authors: Becker Jerome AJ , Pellissier Lucie P , Corde Yannick , Laboute Thibaut , Léauté Audrey , Gandía Jorge , Le Merrer Julie 
Published: June 2020

AbstractBackgroundUnderstanding the neurobiological underpinnings of abstinence from drugs of abuse is critical to allow better recovery and ensure relapse prevention in addicted subjects.MethodsBy comparing the long-term transcriptional consequences of morphine and cocaine exposure, we identified the metabotropic glutamate receptor subtype 4 (mGluR4) as a promising pharmacological target in morphine abstinence. We evaluated the behavioral and molecular effects of facilitating mGluR4 activity in abstinent mice.ResultsTranscriptional regulation of marker genes of medium spiny neurons (MSNs) in the nucleus accumbens (NAc) allowed best discriminating between 4-week morphine and cocaine abstinence. Among these markers,Grm4, encoding mGluR4, displayed down-regulated expression in the caudate putamen and NAc of morphine, but not cocaine, abstinent mice. Remarkably, chronic administration of the mGluR4 positive allosteric modulator (PAM) VU0155041 (2.5 and 5 mg/kg) rescued social abilities, normalized stereotypies and anxiety and blunted locomotor sensitization in morphine abstinent mice. This treatment improved social preference but increased stereotypies in cocaine abstinent mice. Finally, the beneficial behavioral effects of VU0155041 treatment in morphine abstinent animals were correlated with restored expression of key MSN and neural activity marker genes in the NAc.ConclusionsThis study is the first report of relieving effects of a pharmacological treatment, chronic administration of the mGluR4 PAM VU0155041, on long-term deleterious consequences of morphine exposure. It illustrates the neurobiological differences between opiate and psychostimulant abstinence and points to pharmacological repression of excessive activity of D2-MSNs in the NAc as a promising therapeutic lever in drug addiction.
Colloblasts act as a biomechanical sensor for suitable prey inPleurobrachia
Authors: Townsend JP , Merces GOT , Castellanos GP , Pickering M 
Published: June 2020

AbstractCtenophores are a group of largely-planktonic, gelatinous carnivores whose most common method of prey capture is nearly a phylum-defining trait. Tentaculate ctenophores release an unknown proteinaceous adhesive from specialised colloblast cells lining their tentacles following prey contact with the tentacles. There exist no extant studies of the mechanical properties of colloblast adhesive. We use live microscopy techniques to visualise adhesion events betweenPleurobrachia pileuscolloblasts and probes of different surface chemistries in response to probing with varying contact areas. We further define two mechanisms of adhesion termination upon probe retraction. Adapting a technique for measuring surface tension, we examine the adhesive strength of tentacles in the ctenophorePleurobrachia bacheiunder varying pH and bonding time conditions, and demonstrate the destructive exhaustion of colloblast adhesive release. We find that colloblast-mediated adhesion is rapid, and that the bonding process is robust against shifts in ambient pH. However, we find that thePleurobrachiacolloblast adhesive system is among the weakest biological adhesive systems yet described. We place this surprising observation into a broader ecophysiological context by modeling prey capture for prey of a range of sizes. We find that limited use of colloblast adhesive with high surface area contact is suitable both for capturing appropriately sized prey and rejecting, by detachment, prey above a certain size threshold. This allowsPleurobrachia, lacking a mechanism to directly “see” potential prey they are interacting with, to invest in capturing only prey of an appropriate size, decreasing the risk of injury.Summary statementCtenophore colloblast adhesive is found to be strong, but few colloblasts are simultaneously active, producing a weakly-adhering system. A physical model demonstrates how such a system may filter unsuitable prey.
Aligning SARS-CoV-2 Indicators via an Epidemic Model: Application to Hospital Admissions and RNA Detection in Sewage Sludge
Authors: Kaplan Edward H. , Wang Dennis , Wang Mike , Malik Amyn A. , Zulli Alessandro , Peccia Jordan 
Published: June 2020

AbstractAscertaining the state of coronavirus outbreaks is crucial for public health decision-making. Absent repeated representative viral test samples in the population, public health officials and researchers alike have relied on lagging indicators of infection to make inferences about the direction of the outbreak and attendant policy decisions. Recently researchers have shown that SARS-CoV-2 RNA can be detected in municipal sewage sludge with measured RNA concentrations rising and falling suggestively in the shape of an epidemic curve while providing an earlier signal of infection than hospital admissions data. The present paper presents a SARS-CoV-2 epidemic model to serve as a basis for estimating the incidence of infection, and shows mathematically how modeled transmission dynamics translate into infection indicators by incorporating probability distributions for indicator-specific time lags from infection. Hospital admissions and SARS-CoV-2 RNA in municipal sewage sludge are simultaneously modeled via maximum likelihood scaling to the underlying transmission model. The results demonstrate that both data series plausibly follow from the transmission model specified and provide a 95% confidence interval estimate of the reproductive number R0 ≈ 2.4 ±0.2. Sensitivity analysis accounting for alternative lag distributions from infection until hospitalization and sludge RNA concentration respectively suggests that the detection of viral RNA in sewage sludge leads hospital admissions by 3 to 5 days on average. The analysis suggests that stay-at-home restrictions plausibly removed 89% of the population from the risk of infection with the remaining 11% exposed to an unmitigated outbreak that infected 9.3% of the total population.HighlightsA maximum likelihood method for aligning observed lagged epidemic indicators via an underlying transmission model is derived and illustrated using observed COVID-19 hospital admissions and SARS-CoV-2 RNA concentrations measured in sewage sludge to model a local SARS-CoV-2 outbreakThe method enables direct estimation of the reproductive number R0 from the observed indicators along with the initial prevalence of SARS-CoV-2 infection in the population at riskThe analysis suggests tracking SARS-CoV-2 RNA concentration in sewage sludge provides a 3 to 5 day lead time over tracking hospital admissions, consistent with purely statistical time series analysis previously reportedThe model enables estimation of the fraction of the population compliant with government-mandated stay-at-home restrictions, the size of the exposed population, and the fraction of the population infected with SARS-CoV-2 over the outbreak
Endo-lysosomal Aβ concentration and pH enable formation of Aβ oligomers that potently induce Tau missorting
Authors: Schützmann Marie P. , Hasecke Filip , Bachmann Sarah , Zielinski Mara , Hänsch Sebastian , Schröder Gunnar F. , Zempel Hans , Hoyer Wolfgang 
Published: June 2020

AbstractAmyloid-β peptide (Aβ) forms metastable oligomers >50 kD, termed AβOs or protofibrils, that are more effective than Aβ amyloid fibrils at triggering Alzheimer’s disease-related processes such as synaptic dysfunction and Tau pathology, including Tau mislocalization. In neurons, Aβ accumulates in endo-lysosomal vesicles at low pH. Here, we show that the rate of AβO assembly is accelerated 8,000-fold upon pH reduction from extracellular to endo-lysosomal pH, at the expense of amyloid fibril formation. The pH-induced promotion of AβO formation and the high endo-lysosomal Aβ concentration together enable extensive AβO formation of Aβ42 under physiological conditions. Exploiting the enhanced AβO formation of the dimeric Aβ variant dimAβ we furthermore demonstrate targeting of AβOs to dendritic spines, potent induction of Tau missorting, a key factor in tauopathies, and impaired neuronal activity. The results suggest that the endosomal/lysosomal system is a major site for the assembly of pathomechanistically relevant AβOs.
Ancestral reconstructions decipher major adaptations of ammonia oxidizing archaea upon radiation into moderate terrestrial and marine environments
Authors: Abby Sophie S. , Kerou Melina , Schleper Christa 
Published: June 2020

AbstractUnlike all other archaeal lineages, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaea are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here we reconstructed the genomic content and growth temperature of the ancestor of all AOA as well as the ancestors of the marine and soil lineages based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (I) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (II) an expansion of regulatory capacities in transcription and central metabolic functions and (III) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.
Reliability of serological tests for COVID-19: Comparison of three immunochromatography test kits for SARS-CoV-2 antibodies
Authors: Fujigaki Hidetsugu , Takemura Masao , Osawa Michiko , Sakurai Aki , Nakamoto Kentaro , Setod Koichi , Fujita Takashi , Hata Tadayoshi , Akiyama Hidehiko , Doi Yohei , Saito Kuniaki 
Published: June 2020

AbstractBackgroundSeveral immunochromatographic serological test kits have been developed to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibodies, but their relative performance and potential clinical utility is unclear.MethodsThree commercially available serological test kits were evaluated using 99 serum samples collected from 29 patients diagnosed with coronavirus disease 2019 (COVID-19).ResultsThe IgM antibody-positive rates of the three serological test kits for samples taken at the early stage of the disease (0–6 days after onset) were 19.0%, 23.8%, and 19.0%, respectively. The IgM antibody-positive rates over the entire period were 21.2%, 60.6%, and 15.2%, respectively. The IgG antibody-positive rates for samples taken after 13 days of onset were 100.0%, 97.6%, and 97.6%, respectively.ConclusionThere were large differences among the results of the three test kits. Only few cases showed positive results for IgM in the early stage of disease and the IgM antibody-positive rates over the entire period were low, suggesting that the kits used in this study were unsuitable for diagnosis of COVID-19. The IgG antibody was positive in almost all samples after 13 days of onset, suggesting that it may be useful for determining infections in the recent past.
A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples
Authors: Ramos-Mandujano Gerardo , Salunke Rahul , Mfarrej Sara , Rachmadi Andri , Hala Sharif , Xu Jinna , Alofi Fadwa S. , Khogeer Asim , Hashem Anwar M. , Almontashiri Naif A.M. , Alsomali Afrah , Hamdan Samir , Hong Peiying , Pain Arnab , Li Mo 
Published: June 2020

AbstractDiagnosis and surveillance of emerging pathogens such as SARS-CoV-2 depend on nucleic acid isolation from clinical and environmental samples. Under normal circumstances, samples would be processed using commercial proprietary reagents in Biosafety 2 (BSL-2) or higher facilities. A pandemic at the scale of COVID-19 has caused a global shortage of proprietary reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. We developed an open-source method calledMagnetic-nanoparticle-AidedViralRNAIsolation ofContagiousSamples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Unlike conventional methods, MAVRICS works directly in samples inactivated in acid guanidinium thiocyanate-phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. MAVRICS is scalable and thus could become an enabling technology for widespread community testing and wastewater monitoring in the current and future pandemics.
Superspreading in Early Transmissions of COVID-19 in Indonesia
Authors: Hasan Agus , Susanto Hadi , Kasim Muhammad Firmansyah , Nuraini Nuning , Lestari Bony , Triany Dessy , Widyastuti Widyastuti 
Published: June 2020

ABSTRACTWe estimate the basic reproduction numberℛ0and the overdispersion parameter𝒦at two regions in Indonesia: Jakarta-Depok and Batam. Based on the first 1288 confirmed cases in both regions, we find a high degree of individual-level variation in the transmission. The basic reproduction numberℛ0is estimated at 6.79 and 2.47, while the overdispersion parameter𝒦of a negative-binomial distribution is estimated at 0.06 and 0.2 for Jakarta-Depok and Batam, respectively. This suggests that superspreading events played a key role in the early stage of the outbreak, i.e., a small number of infected individuals are responsible for large amounts of COVID-19 transmission.
Association of BMI and Obesity with Composite poor outcome in COVID-19 adult patients: A Systematic Review and Meta-Analysis
Authors: Soeroto Arto Yuwono , Soetedjo Nanny Natalia , Purwiga Aga , Santoso Prayudi , Kulsum Iceu Dimas , Suryadinata Hendarsyah , Ferdian Ferdy 
Published: June 2020

AbstractAimThis study aimed to evaluate the association between obesity and composite poor outcome in coronavirus disease 2019 (COVID-19) patients.MethodsWe conducted a systematic literature search from PubMed and Embase database. We included all original research articles in COVID-19 adult patients and obesity based on classification of Body Mass Index (BMI) and composite poor outcome which consist of mortality, morbidity, admission of Intensive Care Unit (ICU), mechanical ventilation, Acute Respiratory Distress Syndrome (ARDS), and severe COVID-19.ResultsNine studies were included in meta-analysis with 6 studies presented BMI as continuous outcome and 3 studies presented BMI as dichotomous outcome (obese and non-obese). Most studies were conducted in China (55.5%) with remaining studies from French, Germany, and United States (US). COVID-19 patients with composite poor outcome had higher BMI with mean difference 0.55 kg/m2(95% CI 0.07–1.03, P=0.02). BMI ≥30 (obese) was associated with composite poor outcome with odds ratio 1.89 (95% CI 1.06–3.34, P=0.03). Multivariate meta-regression analysis by including three moderators: age, hypertension, and Diabetes Mellitus type 2 (DM type 2) showed the association between obesity and composite poor outcome was affected by age with regression coefficient =-0.06 and P=0.02. Subgroup analysis was not performed due to the limited number of studies for several outcomes.ConclusionObesity is a risk factor of composite poor outcome of COVID-19. On the other hand, COVID-19 patients with composite poor outcome have higher BMI. BMI is an important routine procedure that should be assessed in the management of COVID-19 patients and special attention should be given to patients with obesity.
Structural basis for selective targeting of Rac subfamily GTPases by a bacterial effector protein
Authors: Dietz Nikolaus Balthasar , Huber Markus , Sorg Isabel , Goepfert Arnaud , Harms Alexander , Schirmer Tilman , Dehio Christoph 
Published: June 2020

SummaryRas-homology (Rho) family GTPases are conserved molecular switches controlling fundamental cellular activities in eukaryotic cells. As such, they are targeted by numerous bacterial toxins and effector proteins, which have been intensively investigated regarding their biochemical activities and discrete target spectra; however, molecular mechanisms of target selectivity have remained elusive. Here, we report a bacterial effector protein that targets all four Rac subfamily members of Rho family GTPases, but none of the closely related Cdc42 or RhoA subfamilies. This exquisite target selectivity of the FIC domain AMP-transferase Bep1 fromBartonella rochalimaeis based on electrostatic interactions with a subfamily-specific pair of residues in the nucleotide-binding motif and the Rho insert helix. Residue substitutions at the identified positions in Cdc42 facilitate modification by Bep1, while corresponding Cdc42-like substitutions in Rac1 greatly diminish modification. Our study establishes a structural paradigm for target selectivity towards Rac subfamily GTPases and provides a highly selective tool for their functional analysis.
Improvement of the thrust-torque ratio of an unmanned helicopter by using the ABC algorithm
Authors: Konar Mehmet , Turkmen Aydin , Oktay Tugrul 
Published: June 2020

Purpose
The purpose of this paper is to use an ABC algorithm to improve the thrust–torque ratio of a rotating-wing unmanned aerial vehicle (UAV) model.

Design/methodology/approach
The design of UAVs, such as aircraft, drones, helicopters, has become one of the popular engineering areas with the development of technology. This study aims to improve the value of thrust–torque ratio of an unmanned helicopter. For this purpose, an unmanned helicopter was built at the Faculty of Aeronautics and Astronautics, Erciyes University. The maximum thrust–torque ratio was calculated considering the blade length, blade chord width, blade mass density and blade twist angle. For calculation, artificial bee colony (ABC) algorithm was used. By using ABC algorithm, the maximum thrust–torque ratio was obtained against the optimum input values. For this purpose, a model with four inputs and a single output is formed. In the generated system model, optimum thrust–torque ratio was calculated by changing the input values used in the ±5% range. As a result of this study, approximately 31% improvement was achieved. According to these results, the proposed approach will provide convenience to the designers in the design of the rotating-wing UAV.

Findings
According to these results, approximately 31% improvement was achieved, and the proposed approach will provide convenience to the designers in the design of the rotating-wing UAV.

Research limitations/implications
It takes a long time to obtain the optimum thrust–torque ratio value through the ABC algorithm method.

Practical implications
Using ABC algorithm provides to improve the value of thrust–torque ratio of an unmanned helicopter. With this algorithm, unmanned helicopter flies more than ever. Thus, the presented method based on the ABC algorithm is more efficient.

Social implications
The application of the ABC algorithm method can be used effectively to calculate the thrust–torque ratio in UAV.

Originality/value
Providing an original and penetrating a method that saves time and reduces the cost to improve the value of thrust–torque ratio of an unmanned helicopter.