bluuebunny/crossref_metadata_2025_split huggingface dataset:
Internal control for process monitoring of clinical metagenomic next-generation sequencing of urine samples
Authors: Janes Victoria A. , van der Laan Jennifer S. , Matamoros Sébastien , Mende Daniel R. , de Jong Menno D. , Schultsz Constance 
Published: March 2020

ABSTRACTBackgroundProcess control for clinical metagenomic next-generation sequencing (mNGS) is not yet widely applied, while technical sources of bias are plentiful. We present an easy-to-use internal control (IC) method focussing on technical process control applied to metagenomics in clinical diagnostics.MethodsDNA of nine urine samples was sequenced in the absence and presence ofThermus thermophilusDNA as IC in incremental concentrations (0.5-2-5%). Between aliquots of each sample, we compared the IC relative abundance (RA), and afterin silicosubtraction of IC reads, the microbiota and the RA of pathogens. The optimal IC spike-in concentration was defined as the lowest concentration still detectable in all samples.ResultsThe RA of IC correlated linearly with the spiked IC concentration (r2=0.99). IC added in a concentration of 0.5% of total DNA concentration was detectable in all samples, regardless of human/bacterial composition and afterin silicoremoval gave the smallest difference in RA of pathogens compared to the unspiked aliquot of the sample. The microbiota of sample aliquots sequenced in the presence and absence of IC was highly similar afterin silicoremoval of IC reads (median BC-dissimilarity per sample of 0.059), provided samples had sufficient bacterial read counts.ConclusionT. thermophilusDNA at a percentage of 0.5% of the total DNA concentration can be applied for the process control of mNGS of urine samples. We demonstrated negligible alterations in sample microbial composition afterin silicosubtraction of IC sequence reads. This approach contributes toward implementation of mNGS in the clinical microbiology laboratory.
Evaluating COVID-19 Public Health Messaging in Italy: Self-Reported Compliance and Growing Mental Health Concerns
Authors: Barari Soubhik , Caria Stefano , Davola Antonio , Falco Paolo , Fetzer Thiemo , Fiorin Stefano , Hensel Lukas , Ivchenko Andriy , Jachimowicz Jon , King Gary , Kraft-Todd Gordon , Ledda Alice , MacLennan Mary , Mutoi Lucian , Pagani Claudio , Reutskaja Elena , Roth Christopher , Slepoi Federico Raimondi 
Published: March 2020

AbstractPurposeThe COVID-19 death-rate in Italy continues to climb, surpassing that in every other country. We implement one of the first nationally representative surveys about this unprecedented public health crisis and use it to evaluate the Italian government’ public health efforts and citizen responses.Findings(1) Public health messaging is being heard. Except for slightly lower compliance among young adults, all subgroups we studied understand how to keep themselves and others safe from the SARS-Cov-2 virus. Remarkably, even those who do not trust the government, or think the government has been untruthful about the crisis believe the messaging and claim to be acting in accordance. (2) The quarantine is beginning to have serious negative effects on the population’s mental health.Policy RecommendationsCommunications should move from explaining to citizens that they should stay at home to what they can do there. We need interventions that make staying following public health protocols more desirable, such as virtual social interactions, online social reading activities, classes, exercise routines, etc. — all designed to reduce the boredom of long term social isolation and to increase the attractiveness of following public health recommendations. Interventions like these will grow in importance as the crisis wears on around the world, and staying inside wears on people.
An alternative workflow for molecular detection of SARS-CoV-2 - escape from the NA extraction kit-shortage, Copenhagen, Denmark, March 2020
Authors: Fomsgaard Anna S. , Rosenstierne Maiken W. 
Published: March 2020

AbstractThe World Health Organisation has declared a pandemic caused by the newly discovered SARS-CoV-2. Due to growing demand for reagents used for SARS-CoV-2 RNA extraction for subsequent molecular diagnostics, there is a worldwide risk of kit- and/or reagent-shortages for extraction. With a detection sensitivity of 97.4% (95% CI=86.2-99.9%), we describe a simple, fast, alternative workflow for molecular detection of SARS-CoV-2, where samples are simply heat-processed for 5 minutes at 98°C prior to the RT-qPCR reaction.
A COVID-19 Infection Risk Model for Frontline Health Care Workers
Authors: Dy Louie Florendo , Rabajante Jomar Fajardo 
Published: March 2020

AbstractThe number of confirmed COVID-19 cases admitted in hospitals is continuously increasing in the Philippines. Frontline health care workers are faced with imminent risks of getting infected. In this study, we formulate a theoretical model to calculate the risk of being infected in health care facilities considering the following factors: the average number of encounters with a suspected COVID-19 patient per hour; interaction time for each encounter; work shift duration or exposure time; crowd density, which may depend on the amount of space available in a given location; and availability and effectiveness of protective gears and facilities provided for the frontline health care workers. Based on the simulation results, a set of risk assessment criteria is proposed to classify risks as ‘low’, ‘moderate’, or ‘high’. We recommend the following: (i) decrease the rate of patient encounter per frontline health care worker, e.g., maximum of three encounters per hour in a 12-hour work shift duration; (ii) decrease the interaction time between the frontline health care worker and the patients, e.g., less than 40 minutes for the whole day; (iii) increase the clean and safe space for social distancing, e.g., maximum of 10% crowd density, and if possible, implement compartmentalization of patients; and/or (iv) provide effective protective gears and facilities, e.g., 95% effective, that the frontline health care workers can use during their shift. Moreover, the formulated model can be used for other similar scenarios, such as identifying infection risk in public transportation, school classroom settings, offices, and mass gatherings.
Gestational-age-dependent development of the neonatal metabolome
Authors: Ernst Madeleine , Rogers Simon , Lausten-Thomsen Ulrik , Björkbom Anders , Laursen Susan Svane , Courraud Julie , Børglum Anders , Nordentoft Merete , Werge Thomas , Mortensen Preben Bo , Hougaard David M , S.Cohen Arieh 
Published: March 2020

AbstractBackgroundPrematurity is a severe pathophysiological condition associated with increased morbidity and mortality; however, little is known about the gestational-age-dependent development of the neonatal metabolome.MethodsUsing an untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS) metabolomics protocol we measured over 6000 metabolites in 148 neonatal heel prick dried blood spots retrieved from the Danish Neonatal Screening Biobank. Using a combination of state-of-the-art metabolome mining tools, including mass spectral molecular networking (GNPS), unsupervised substructure discovery (MS2LDA) andin silicostructure annotation, we retrieved chemical structural information at a broad level for over 4000 (60%) metabolites and assessed their relation to gestational age.ResultsA total of 744 (∼12%) metabolites were significantly correlated with gestational age (false-discovery-rate-adjustedP< 0.05), whereas 93 metabolites were strongly predictive of gestational age, explaining on average 37% of the variance. Using a custom algorithm based on hypergeometric testing we identified 17 molecular families (230 metabolites) overrepresented with metabolites correlating with gestational age (P< 0.01). Metabolites significantly related to gestational age included bile acids, carnitines, polyamines, amino-acid-derived compounds, nucleotides, dipeptides as well as treatment-related metabolites such as antibiotics and caffeine.ConclusionsCarnitines, bile acids, as well as amino acid-derived compounds are known to be affected by the gut microbiota, whereas polyamines such as spermine and spermidine may play an important role in regulating (epithelial) cell growth. Our findings reveal for the first time the gestational-age-dependent development of the neonatal blood metabolome and suggest that gut microbial and gestational-age-dependent metabolic maturation may be monitored during newborn screening.
Potential roles of social distancing in mitigating the spread of coronavirus disease 2019 (COVID-19) in South Korea
Authors: Park Sang Woo , Sun Kaiyuan , Viboud Cécile , Grenfell Bryan T. , Dushoff Jonathan 
Published: March 2020

AbstractOn January 20, 2020, the first COVID-19 case was confirmed in South Korea. After a rapid outbreak, the number of incident cases has been consistently decreasing since early March; this decrease has been widely attributed to its intensive testing. We report here on the likely role of social distancing in reducing transmission in South Korea. Our analysis suggests that transmission may still be persisting in some regions.
In Vivo Localization of Deep Brain Implants in Mice
Authors: Király Bálint , Balázsfi Diána , Horváth Ildikó , Solari Nicola , Sviatkó Katalin , Lengyel Katalin , Birtalan Eszter , Máthé Domokos , Szigeti Krisztián , Hangya Balázs 
Published: March 2020

AbstractElectrophysiology provides a direct readout of neuronal activity at a temporal precision only limited by the sampling rate. However, interrogating deep brain structures, implanting multiple targets or aiming at unusual angles still poses significant challenges even for expert operators, and errors are only discovered by post-hoc histological reconstruction. Here, we propose a method combining the high-resolution information about bone landmarks provided by micro-CT scanning with the soft tissue contrast of the MRI, which allowed us to precisely localize electrodes and optic fibers in mice in vivo. This enables arbitrating the success of implantation directly after surgery with a precision comparable to the gold standard histological reconstruction. Adjustment of the recording depth with electrode microdrives or early termination of unsuccessful experiments saves many working hours, while fast 3-dimensional feedback helps surgeons to avoid systematic errors. Increased aiming precision will allow more precise targeting of small or deep brain nuclei and multiple targeting of specific cortical layers.
Introductory gestures before songbird vocal displays are shaped by learning and biological predispositions
Authors: Kalra Shikha , Yawatkar Vishruta , James Logan S , Sakata Jon T , Rajan Raghav 
Published: March 2020

ABSTRACTIntroductory gestures are present at the beginning of many animal displays. For example, lizards start their head-bobbing displays with introductory push-ups and animal vocal displays begin with introductory notes. Songbirds also begin their vocal displays by repeating introductory notes (INs) before producing their learned song and these INs are thought to reflect motor preparation. Between individuals of a given species, the acoustic structure of INs and the number of times INs are repeated before song varies considerably. While similar variation in songs between individuals is known to be a result of learning, whether INs are also learned remains poorly understood. Here, using natural and experimental tutoring with male zebra finches, we show that mean IN number and IN acoustic structure are learned from a tutor, independent of song learning. We also reveal biological predispositions in IN production; birds artificially tutored with songs lacking INs still repeated a short-duration syllable, thrice on average, before their songs. Overall, these results show that INs, just like elements in song, are shaped both by learning and biological predispositions and suggest multiple, independent, learning processes underlying the acquisition of complex vocal displays.
Bipartite network analysis of ant-task associations reveals task groups and absence of colonial daily activity
Authors: Fujioka Haruna , Okada Yasukazu , Abe Masato S. 
Published: March 2020

AbstractSocial insects are one of the best examples of complex self-organised systems exhibiting task allocation. How task allocation is achieved is the most fascinating question in behavioural ecology and complex systems science. However, it is difficult to comprehensively characterise task allocation patterns due to behavioural complexity, such as the individual variation, context dependency, and chronological variation. Thus, it is imperative to quantify individual behaviours and integrate them into colony levels. Here, we applied bipartite network analyses to characterise individual-behaviour relationships. We recorded the behaviours of all individuals with verified age in ant colonies and analysed the individual-behaviour relationship at the individual, module, and network levels. Bipartite network analysis successfully detected the module structures, illustrating that certain individuals performed a subset of behaviours (i.e., task groups). We confirmed age polyethism by comparing age between modules. Additionally, to test the daily rhythm of the executed tasks, the data were partitioned between daytime and nighttime, and a bipartite network was re-constructed. This analysis supported that there was no daily rhythm in the tasks performed. These findings suggested that bipartite network analyses could untangle complex task allocation patterns and provide insights into understanding the division of labour.
A Comprehensive Survey of Mutations in Oesophageal Carcinoma Reveals Recurrent Neoantigens as Potential Immunotherapy Targets
Authors: Chen Chao , Liu Songming , Xiong Heng , Zhang Xi , Li Bo 
Published: March 2020

AbstractThis study was aimed to investigate the mutations in Esophageal Carcinoma (EC) for recurrent neoantigen identification. A total of 733 samples with whole exome sequencing (WES) mutation data and 1153 samples with target region sequencing data were obtained from 7 published studies and GENIE database. Common HLA-I and HLA-II genotypes in both TCGA cohort and Chinese were used to predict the probability of ‘public’ neoantigens in the dataset. Based on the integrated data, we not only obtained the most comprehensive EC mutation landscape so far, but also found 253 mutation sites which could be identified in at least 3 or more patients, including,TP53p.R248Q,PIK3CAp.E545K,PIK3CAp.E542K,KRASp.G12D,PIK3CAp.H1047R andTP53p.C83F. These mutations can be recognized by multiple common HLA molecules (HLA-A11:01, HLA-B57:01, HLA-A03:01, DRB1-0301, DRB1-1202, et al.) in Chinese and TCGA cohort as potential public neoantigens. Overall, our analysis provides some potential targets for EC immunotherapy.
Simple and Robust Fabrication and Characterization of Conductive Carbonized Nanofibers Loaded with Gold Nanoparticles for Bone Tissue Engineering Applications
Authors: Nekounam Houra , Gholizadeh Shayan , Allahyari Zahra , Mirzaei Esmaeil , Shokrgozar Mohammad Ali , Faridi-Majidi Reza 
Published: March 2020

AbstractBone tissue engineering is a new and applicable emerging approach to repair the bone defects. In this regard, designing and robust fabrication of tissue engineering scaffolds that could provide an appropriate environment for cell proliferation and differentiation is of high interest. Electrical conductive scaffolds which provide a substrate for stimulating cell growth and differentiation through a physiologically relevant physical signaling, electrical stimulation, has shown a highly promise in this approach. In this paper, we fabricated carbon nanofiber/gold nanoparticle (CNF/GNP) conductive scaffolds using two distinct methods; blending electrospinning in which gold nanoparticles were blended with electrospinning solution and electrospun, and electrospinning/electrospraying in which gold nanoparticle was electrosprayed simultaneously with electrospinning. The obtained electrospun mats underwent stabilization/carbonization process to prepare CNF/GNP scaffolds. The scaffolds were characterized by SEM, XRD, and Raman spectroscopy. SEM characterizations showed improved morphology and a slight decrease in the diameter of the spinned and sprayed nanofibers with moderate concentrations (from 178.66 ± 38.40 nm to 157.94 ± 24.14 nm and 120.81 ± 13.77 nm, respectively), In the electrosprayed form, better size distributions of nanofibers and less adhesion between individual fibers was observed, while XRD analysis confirmed the crystal structure of the nanofibers. Raman spectroscopy revealed enhancement in the graphitization of the structure, and the electrical conductivity of the structure improved by up to 29.2% and 81% in electrospraying and blending electrospinning modes, respectively. Indirect MTT and LDH toxicity assays directly were performed to assess MG63 cell toxicity, but no significant toxicity was observed and the scaffolds did not adversely affect cell proliferation. Overall, it can be concluded that in early tests, this structure have significant potential for bone tissue engineering applications.Abstract FigureFigure 1:
The time-series ages distribution of the reported COVID-2019 infected people suggests the undetected local spreading of COVID-2019 in Hubei and Guangdong provinces before 19th Jan 2020
Authors: Wu Chao , Zheng Min 
Published: March 2020

AbstractCOVID-2019 is broken out in China. It becomes a severe public health disaster in one month. Find the period in which the spreading of COVID-2019 was overlooked, and understand the epidemiological characteristics of COVID-2019 in the period will provide valuable information for the countries facing the threats of COVID-2019. The most extensive epidemiological analysis of COVID-2019 shows that older people have lower infection rates compared to middle-aged persons. Common sense is that older people prefer to report their illness and get treatment from the hospital compared to middle-aged persons. We propose a hypothesis that when the spreading of COVID-2019 was overlooked, we will find more older cases than the middle-aged cases.At first, we tested the hypothesis with 4597 COVID-2019 infected samples reported from 26th Nov 2019 to 17th Feb 2020 across the mainland of China. We found that 19th Jan 2020 is a critical time point. Few samples were reported before that day, and most of them were older ones. Then samples were explosively increased after that day, and many of them were middle-aged people. We have demonstrated the hypothesis to this step.Then, we grouped samples by their residences(provinces). We found that, in the provinces of Hubei and Guangdong, the ages of samples reported before 19th Jan 2020 are significantly higher than the ages of samples reported after that day. It suggests the COVID-2019 may be spreading in Hubei and Guangdong provinces before 19th Jan 2020 while people were unconscious of it.At last, we proposed that the ages distribution of each-day-reported samples could serve as a warning indicator of whether all potential COVID-2019 infected people are found.We think the power of our analysis is limit because 1. the work is data-driven, and 2. only ∼5% of the COVID-2019 infected people in China are included in the study. However, we believe it still shows some value for its ability to estimate the possible unfound COVID-2019 infected people.
Disposable N95 Masks Pass Qualitative Fit-Test But Have Decreased Filtration Efficiency after Cobalt-60 Gamma Irradiation
Authors: Cramer Avilash , Tian Enze , Yu Sherry H. , Galanek Mitchell , Lamere Edward , Li Ju , Gupta Rajiv , Short Michael P. 
Published: March 2020

ABSTRACTThe current COVID-19 pandemic has led to a dramatic shortage of masks and other personal protective equipment (PPE) in hospitals around the globe [1]. One component of PPE that is in particular demand are disposable N95 face masks. To alleviate this, many methods of N95 mask sterilization have been studied and proposed with the hope of being able to safely reuse masks [2]. Two major considerations must be made when re-sterilizing masks: (1) the sterilization method effectively kills pathogens, penetrating into the fibers of the mask, and (2) the method does not degrade the operational integrity of the N95 filters.We studied Cobalt-60 (60Co) gamma irradiation as a method of effective sterilization without inducing mask degradation. Significant literature exists supporting the use of gamma radiation as a sterilization method, with viral inactivation of SARS-CoV reported at doses of at most 10 kGy [3], with other studies supporting 5 kGy for many types of viruses [4]. However, concerns have been raised about the radiation damaging the fiber material within the mask, specifically by causing cross-linking of polymers, leading to cracking and degradation during fitting and/or deployment [5, 6].A set of 3M 8210 and 9105 masks were irradiated using MIT’s 60Co irradiator. Three masks of each type received 0 kiloGray (kGy), 10 kGy and 50 kGy of approximately 1.3 MeV gamma radiation from the circular cobalt sources, at a dose rate of 2.2kGy per hour.Following this sterilization procedure, the irradiated masks passed a OSHA Gerson Qualitative Fit Test QLFT 50 (saccharin apparatus) [7] when donned correctly, performed at the Brigham and Women’s Hospital, in a blinded study repeated in triplicate. However, the masks’ filtration of 0.3 µm particles was significantly degraded, even at 10 kGy.These results suggest against gamma, and possibly all ionizing radiation, as a method of disposable N95 sterilization. Even more importantly, they argue against using the qualitative fit test alone to assess mask integrity.
The comparative superiority of IgM-IgG antibody test to real-time reverse transcriptase PCR detection for SARS-CoV-2 infection diagnosis
Authors: Liu Rui , Liu Xinghui , Han Huan , Shereen Muhammad Adnan , Niu Zhili , Li Dong , Liu Fang , Wu Kailang , Luo Zhen , Zhu Chengliang 
Published: March 2020

AbstractBackgroundAs the increasing number of Corona Virus Disease 2019 (COVID-19) patients caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2), which caused an outbreak initiated from Wuhan, China in December, 2019, the clinical features and treatment of COVID-19 patients have been understood. However, it is urgent to need the rapid and accurate detection for SARS-CoV-2 infection diagnosis. We aimed to evaluate the antibodies-based and nucleic acid-based tests (NAT) for SARS-CoV-2-infected patients.MethodWe retrospectively and observationally studied 133 patients diagnosed with SARS-CoV-2 and admitted in Renmin Hospital of Wuhan University, China, from Feb 17 to Mar 1, 2020. Demographic data, symptoms, clinical examination, laboratory tests, and clinical outcomes were collected. Data were compared between IgM-IgG antibody test and real-time RT-PCR detection for COVID-19 patients.ResultsOf 133 patients with SARS-CoV-2 infection, there were 44 moderate cases, 52 severe cases, and 37 critical cases with no significant difference of gender and age among three subgroups. Overall, the positive ratio in IgM antibody test was higher than in RT-PCR detection. In RT-PCR detection, the positive ratio was 65.91%, 71.15%, and 67.57% in moderate, severe, and critical cases, respectively. Whereas, the positive ratio of IgM/IgG antibody detection in patients was 79.55%/93.18%, 82.69%/100%, and 72.97%/97.30% in moderate, severe, and critical cases, respectively. Moreover, the concentrations of antibodies were also measured in three subgroups.ConclusionThe IgM-IgG antibodies-based test exhibited a comparative superiority to the NAT for COVID-19 diagnosis, which provides an effective complement to the false negative results from NAT for SARS-CoV-2 infection diagnosis.