bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survey of Core Facilities shows the importance of communication and management for optimal research quality
Authors: Kos-Braun IC , Gerlach B , Pitzer C 
Published: August 2020

AbstractRecently, it has become evident that academic research faces issues with the reproducibility of research data. It is critical to understand the underlying causes in order to remedy this situation. Core Facilities (CFs) have a central position in the research infrastructure and therefore they are ideally suited to promote and disseminate good research standards through their users. However, there are currently no clear guidelines directly applicable to academic CFs. To identify the most important factors for research quality, we polled 253 CFs across Europe about their practices and analysed in detail the interaction process between CFs and their users, from the first contact to the publication of the results. Although the survey showed that CFs are dedicated to train and advise their users, it highlighted the following areas, the improvement of which would directly increase research quality: 1) motivating users to follow the advice and procedures for best research practice, 2) providing clear guidance on data management practices, 3) improving communication along the whole research process and 4) clearly defining the responsibilities of each party.
Diagnosis of SARS-CoV-2 in children: accuracy of nasopharyngeal swab compared to nasopharyngeal aspirate
Authors: Di Pietro Giada Maria , Capecchi Ester , Luconi Ester , Lunghi Giovanna , Bosis Samantha , Bertolozzi Giuseppe , Cantoni Barbara , Marano Giuseppe , Boracchi Patrizia , Biganzoli Elia , Castaldi Silvana , Marchisio Paola , Gori Andrea , Agostoni Carlo , Pinzani Raffaella , Ceriotti Ferruccio 
Published: August 2020

AbstractThe tests currently used for the direct identification of SARS-CoV-2 include specimens taken from upper and lower respiratory tract; recommendations from Word Health Organization prioritise nasopharyngeal swab (NS). In literature there are not available paediatric studies about the identification of SARS-CoV-2 through nasopharyngeal aspirate (NPA), but the use of NPA is deemed to be better than NS to identify respiratory viruses in children. The aim of our study is to evaluate diagnostic performances of NS compared to NPA for the detection of SARS-CoV-2 in children. We collected 300 paired samples (NS and NPA) from children hospitalized and followed up in our paediatric unit. We calculated the sensitivity and specificity of NS referred to NPA of the whole sample and then, considering both the age (≥ and < 6 years old) and the period of collection (March vs follow up) as covariates in different analysis. The NS has a low sensitivity in detecting SARS-CoV-2 in children when referred to NPA; whereas its specificity results high. In children under 6 years of age, our results suggest to prefer the collection of NS, whenever possible. Though statistically not significant, the sensitivity of NS becomes higher if it is performed before NPA.
A distinct fingerprint of inflammatory mediators and miRNAs inPlasmodium vivaxsevere thrombocytopenia
Authors: Santos Marina L. S. , Coimbra Roney S. , Sousa Tais N. , Guimarães Luiz F. F. , Gomes Matheus S. , Amaral Laurence R. , Pereira Dhelio B. , Fontes Cor J. F. , Hawwari Ibrahim , Franklin Bernardo S. , Carvalho Luzia H. 
Published: August 2020

AbstractBackgroundSevere thrombocytopenia can be a determinant factor in the morbidity ofPlasmodium vivax(Pv), the most widespread human malaria. Although immune mechanisms may drivePv-induced severe thrombocytopenia (PvST), the current data on the cytokine landscape in PvST is scarce, and often conflicting. The analysis of the bidirectional circuit of inflammatory mediators and miRNAs would lead to a better understanding of the mechanisms underlying PvST.MethodsWe combined Luminex proteomics, NanoString miRNA quantification, and machine learning, to evaluate an extensive array of plasma mediators in uncomplicatedPvpatients, whose blood platelet counts varied from reference values to PvST.ResultsUnsupervised clustering analysis identified PvST-linked signatures comprised of both inflammatory (CXCL10, CCL4, and IL-18) and regulatory (IL-10, IL-1Ra, HGF) mediators. As part of PvST signatures, IL-6 and IL-8 were critical to discriminatePvsubgroups, while CCL2 and IFN-γ from healthy controls. Supervised machine learning spotlighted IL-10 inPv-mediated thrombocytopenia, and provided evidence for a potential signaling route involving IL-8 and HGF. Finally, we identified a set of miRNAs capable of modulating these signaling pathways.ConclusionsThe results place IL-10 and IL-8/HGF in the center of PvST and propose investigating these signaling pathways across the spectrum of malaria infections.
Impressions of Vibrotactile Signals in Older Adults With and Without History of Stroke
Authors: Seim Caitlyn E. , Ritter Brandon , Flavin Kara E. , Lansberg Maarten G. , Okamura Allison M. 
Published: August 2020

AbstractVibrotactile feedback is mechanical stimulation produced using actuators in contact with the body. The stimulation parameters (frequency, amplitude, location, duration) can be adjusted to produce a variety of sensations. By characterizing how users respond to different settings, interaction designers can create more usable and enjoyable haptic interfaces. This form of haptic feedback is being used widely for alerts, gaming, and simulation; however, emerging technologies in the fields of brain health and physical therapy are introducing new users to this stimulation. For applications using vibrotactile stimulation to advance, researchers are studying perceived sensations and affective response. However, these studies often focus on healthy, younger users. It is well known that older adults and those with acquired brain injury have different physiology and different perception than young adults. Here we present a set of vibrotactile signals to adults over 40 years old with and without history of stroke and query affective impression and experienced sensations. Signals on the palm and those with a changing stimulus location were associated with higher valence ratings, while low-amplitude signals showed lowest arousal. Users preferred stimulation that they could perceive, and they could not perceive most signals applied to the forearm. Reported sensations include tickle, tingling, and numbness.CCS ConceptsHuman-centered computing → User studies; Haptic devices; Ubiquitous and mobile devices.
Insulin-like growth factor 1 signaling in the placenta requires endothelial nitric oxide synthase to support trophoblast function and normal fetal growth
Authors: Wilson Rebecca L , Troja Weston , Sumser Emily K , Maupin Alec , Lampe Kristin , Jones Helen N 
Published: August 2020

AbstractCurrently, there is no effective treatment for placenta dysfunctionin utero. In a ligated mouse model of fetal growth restriction (FGR), nanoparticle-mediatedhuman insulin-like 1 growth factor(hIGF1) gene delivery (NP-Plac1-hIGF1) increasedhIGF1expression and maintained fetal growth. However, whether it can restore fetal growth remains to be determined. Using the endothelial nitric oxide synthase knockout (eNOS−/−) mouse model, a genetic model of FGR, we found that despite inducing expression ofhIGF1in the placentas treated with NP-Plac1-hIGF1 (P=0.0425), FGR did not resolve. This was associated with no change to the number of fetal capillaries in the placenta labyrinth; an outcome increased with NP-Plac1-hIGF1 treatment in the ligated mouse model, despite increased expression of angiopoietin 1 (P=0.05) and suggestedIGF1signaling in the placenta requires eNOS to modulate placenta angiogenesis. To further assess this hypothesis, we used the BeWo Choriocarcinoma cell line and human placenta explant cultures that were treated with NP-Plac1-hIGF1, oxidative stress was induced with hydrogen peroxide (H2O2) and NOS activity inhibited using the inhibitor L-NMMA. In both BeWo and explants, the protective effect of NP-Plac1-hIGF1 treatment against H2O2induced cell death/lactate dehydrogenase release was prevented by eNOS inhibition (P=0.003 and P<0.0001, respectively). This was associated with an increase in mRNA expression of oxidative stress markersHIF1α(P<0.0001) andADAM10(P=0.0002) in the NP-Plac1-hIGF1+H2O2+L-NMMA treated BeWo cells. These findings show for the first time the requirement of eNOS/NOS in IGF1 signaling in placenta cells that may have implications for placental angiogenesis and fetal growth.
Teamwork in the manufacturing workplace may hinder social distance
Authors: Kokubun Keisuke 
Published: August 2020

AbstractThe spread of new coronavirus (COVID-19) infections show no signs of stopping. Therefore, if the era of With-Colona will continue for a while, we must consider how to deal with this disaster well. The practice of social distance is one of the powerful tools for that purpose. In previous research, analysis of the factors that influence social distance has also been carried out using information from the US occupation information site O*NET. However, they targeted all industries, not specific industries. Therefore, in this paper, we analyzed the factors that influence Physical Proximity in the manufacturing industry, which has a large impact on the economy given the scale of employment. As the method, first, exploratory factor analysis is performed using O*NET information, and the extracted 7 variables, Sitting Work, Adverse Conditions, Information Processing, Bridging Work, Teamwork, Response to Aggression, and Intelligent Work, are used in the regression analysis. As a result, it was shown that Teamwork is the biggest factor that influences Physical Proximity. Also, Adverse Conditions and Response to Aggression showed a positive correlation and Sitting Work showed a negative correlation. By job type, Maintenance, Installation & Repair tended to have higher Physical Proximity than Manufacturing Production Process Development, Production & Quality Assurance. Keywords: New Coronavirus (COVID-19), social distance, physical proximity, teamwork, explanatory factor analysis, O*NET
Declining SARS-CoV-2 PCR sensitivity with time and dependence on clinical features: consequences for control
Authors: Bergmans B.J.M. , Reusken C.B.E.M. , van Oudheusden A.J.G. , Godeke G.J. , Marinović A.A. Bonačić , de Vries E. , Kluiters-de Hingh Y.C.M. , Vingerhoets R. , Berrevoets M.A.H. , Verweij J.J. , Nieman A.E. , Reimerink J. , Murk J.L. , Swart A.N. 
Published: August 2020

AbstractReal-time reverse transcription-polymerase chain reaction (RT-PCR) on upper respiratory tract (URT) samples is the primary method to diagnose SARS-CoV-2 infections and guide public health measures, with a supportive role for serology. However, the clinical sensitivity of RT-PCR remains uncertain. In the present study, Bayesian statistical modeling was used to retrospectively determine the sensitivity of RT-PCR using SARS-CoV-2 serology in 644 COVID-19-suspected patients with varying degrees of disease severity and duration. The sensitivity of RTPCR ranged between 79–95%; while increasing with disease severity, it decreased rapidly over time in mild COVID-19 cases. Negative URT RT-PCR results should therefore be interpreted in the context of clinical characteristics, especially with regard to containment of viral transmission based on the ‘test, trace and isolate’ principle.
Knowledge and Risk Perception of the Novel Coronavirus Disease among Adult Population in Nigeria: A cross-sectional study
Authors: Hedima Erick Wesley , Michael Samuel Adeyemi , David Emmanuel Agada 
Published: August 2020

AbstractCOVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly infectious disease declared a pandemic by the World Health Organization. The risks of getting infected with the novel coronavirus in Nigeria is high as evident by the increase in the daily number of confirmed cases.ObjectiveThe objectives of this study were to assess the knowledge and risk perception of adult Nigerian population regarding the novel coronavirus pandemic.MethodsWe conducted an online cross-sectional survey in which five hundred and ten (510) adult participants consented and filled the questionnaire. The questionnaire is divided in to four sections: the first part was directed at the socio-demographic characteristics of the participants, the second was dedicated to the assessment of knowledge, the third part assessed risk perception and the fourth section assessed preventive measures.ResultsAlmost all of the participants (95.9%) claimed to be aware of COVID-19 with majority through the traditional media (55.3%), and social media (41%) while only a small percentage (3.7%) gained the awareness through health officials. Knowledge of COVID-19 was significantly poor among participants with lower level of formal education, (p = 0.0001). participants with higher income were found to have a good knowledge of the disease (p< 0.00001). being a health worker was not associated with good knowledge of COVID-19 (p = 0.00001). Risk perception was significantly high among the females (p = 0.044), young adult participants (p = 0.039) and healthcare workers (p = 0.001). Preventive measures like avoiding eating out (p = 0.001) and traveling to high risk areas (p = 0.017), wearing face mask (p = 0.01) and eating balanced diet (p = 0.014) were statistically significant across gender.ConclusionIn general, participants were aware of COVID-19 with a low proportion having a good knowledge about the disease and preventive measures. The findings from this online survey could guide information campaigns by public health authorities, clinicians, and the media.
COVID-19: Estimation of the Actual Onset of Local Epidemic Cycles, Determination of Total Number of Infective, and Duration of the Incubation Period
Authors: de Carvalho Rogerio Atem , de Carvalho Eduardo Atem 
Published: August 2020

AbstractBackgroundMost studies of the epidemic cycles of the pandemic of Sars-CoV-2, or COVID-19 as it became known, define the beginning of specific cycles in countries from the laboratory identification of the first cases of infection, however, there is the awareness that cycles may have started earlier, without proper identification. This influences all the parameters that govern the statistical models used for controlling the infection.PurposeThis work proposes two models based on experimental data. The Logistic Model it is used to obtain three parameters of the epidemic cycle of COVID-19, namely: the final count for the total infected, the daily infection rate and the lag time. Complimentary, a novel inventory model is proposed to calculate the number of infective persons, as well as to determine the incubation period.MethodsThe data on epidemic cycles of Germany, Italy, and Sweden are treated previously by the Moving Average Method with Initial value (MAMI), then a variation of the Logistic Model, obtained through curve-fitting, is used to obtain the three parameters. The inventory model is introduced to calculate the actual number of infected persons and the behavior of the incubation period is analyzed.ResultsAfter comparing data from the three countries it is possible to determine the actual probable dates of the beginning of the epidemic cycles for each one, determine the size of the incubation period, as well as to determine the total number of infective persons during the cycle.ConclusionsThe actual probable dates of the beginning of the epidemic cycles in the countries analyzed are determined, the total number of infected is determined, and it is statistically proven that the incubation cycle for Sars-CoV-2 is five days.
Clinical Impact of Panel Based Error Corrected Next Generation Sequencing versus Flow Cytometry to Detect Measurable Residual Disease (MRD) in Acute Myeloid Leukemia (AML)
Authors: Patkar Nikhil , Kakirde Chinmayee , Shaikh Anam Fatima , Salve Rakhi , Bhanshe Prasanna , Chatterjee Gaurav , Rajpal Sweta , Joshi Swapnali , Chaudhary Shruti , Kodgule Rohan , Ghoghale Sitaram , Deshpande Nilesh , Shetty Dhanalaxmi , Khizer Syed Hasan , Jain Hasmukh , Bagal Bhausaheb , Menon Hari , Khattry Navin , Sengar Manju , Tembhare Prashant , Subramanian Papagudi , Gujral Sumeet 
Published: August 2020

AbstractWe accrued 201 patients of adult AML treated with conventional therapy, in morphological remission and evaluated MRD using sensitive error corrected next generation sequencing (NGS-MRD) and multiparameter flow cytometry (FCM-MRD) at the end of induction (PI) and consolidation (PC). Nearly 71% of patients harbored PI NGS-MRD and 40.9% harbored PC NGS-MRD (median VAF 0.76%). Patients harboring NGS-MRD had a significantly higher cumulative incidence of relapse (p=0.003), inferior overall survival (p=0.001) and relapse free survival (p<0.001) as compared to NGS-MRD negative patients. NGS-MRD was predictive of inferior outcome in intermediate cytogenetic risk and demonstrated potential in favorable cytogenetic risk AML. Patients who cleared PI NGS-MRD had a significantly improved survival as compared to patients who became negative subsequently indicating that kinetics of NGS-MRD clearance was of paramount importance. NGS-MRD identified over 80% of cases identified by flow cytometry at PI time point whereas FCM identified 49.3% identified by NGS. Only a fraction of cases were truly missed by NGS as compared to FCM-MRD. NGS-MRD emerged as the most important independent prognostic factor predictive of inferior outcome (p<0.001). We demonstrate a widely applicable, scalable NGS-MRD approach that is clinically informative and advantageous when compared to FCM-MRD in AML treated with conventional therapies.
3D Printed N95 Equivalent for PPE Shortages: The Kansas City Mask
Authors: Dalla Shiv , Bacon Brandon , Ayres Jack , Holmstead Stephen , Elliot Alan J. Ahlberg 
Published: August 2020

ABSTRACTIntroductionDuring the COVID-19 pandemic, the shortage of personal protective equipment (PPE) was well-reported and discussed, not only in the healthcare sector but across all of society as the demands for PPE skyrocketed. As hospitalizations for COVID-19-related illness continue to increase, many recent reports indicate the supply of PPE is persistently and significantly less than the demand. These PPE shortages encouraged communities of 3D printing experts and hobbyists to design and distribute homemade, 3D-printed PPE, including N95 mask substitutes. The mask presented, the Kansas City Mask (KC Mask), is one such product which was created from the maker community in partnership with local physicians and hospitals. This report discusses the design, manufacturing, and validation of the KC Mask design and its usage in the COVID-19 pandemic as well as future use as stopgap PPE.MethodsThe KC Mask was adapted from a similar design called the Montana Mask. Mask components were 3D printed and assembled then fit tested by qualitative fit testing (QLFT) at Truman Medical Center in Kansas City, MO as a proof of concept.ResultsThe QLFT was successful and the KC Mask was approved for use by pandemic response administration staff at the hospital. Fortunately, the KC Mask has not required wide utilization, however, because supply chains for Kansas City area hospitals have, at the time of this publication, not yet been exhausted by the pandemic.ConclusionThe results of Truman Medical Center’s approval of the KC Mask are promising for this N95 stop-gap substitute. Although further analysis and study is needed for this design, persistently increasing caseloads and PPE shortages necessitate an urgent dissemination of these preliminary results. The authors do not advocate for the KC Mask as a replacement of traditional N95 masks or other PPE but do endorse the KC Mask as a stopgap measure, proven to be effective in situations of dire PPE shortage based on CDC guidelines.
A negative feedback model to explain regulation of SARS-CoV-2 replication and transcription
Authors: Gao Shan , Cheng Zhi , Jin Xiufeng , Wang Fang , Xuan Yibo , Zhou Hao , Liu Chang , Ruan Jishou , Duan Guangyou , Li Xin 
Published: August 2020

AbstractBackgroundCoronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a preliminary understanding of the replication and transcription mechanisms of SARS-CoV-2 has recently emerged, their regulation remains unclear.ResultsBased on reanalysis of public data, we propose a negative feedback model to explain the regulation of replication and transcription in—but not limited to—SARS-CoV-2. The key step leading to new discoveries was the identification of the cleavage sites of nsp15—an RNA uridylate-specific endoribonuclease, encoded by CoVs. According to this model, nsp15 regulates the synthesis of subgenomic RNAs (sgRNAs) and genomic RNAs (gRNAs) by cleaving transcription regulatory sequences in the body. The expression level of nsp15 determines the relative proportions of sgRNAs and gRNAs, which in turn change the expression level of nps15 to reach equilibrium between the replication and transcription of CoVs.ConclusionsThe replication and transcription of CoVs are regulated by a negative feedback mechanism that influences the persistence of CoVs in hosts. Our findings enrich fundamental knowledge in the field of gene expression and its regulation, and provide new clues for future studies. One important clue is that nsp15 may be an important and ideal target for the development of drugs (e.g. uridine derivatives) against CoVs.
TimTrack: A drift-free algorithm for estimating geometric muscle features from ultrasound images
Authors: van der Zee Tim J. , Kuo Arthur D. 
Published: August 2020

AbstractUltrasound imaging is valuable for non-invasively estimating fascicle lengths and other features of pennate muscle, especially when performed computationally. Effective analysis techniques to date typically use optic flow to track displacements from image sequences, but are sensitive to integration drift for longer sequences. We here present an alternative algorithm that objectively estimates geometric features of pennate muscle from ultrasound images, without drift sensitivity. The algorithm identifies aponeuroses and estimates fascicle angles to derive fascicle lengths. Length estimates of human vastus lateralis and lateral gastrocnemius in healthy subjects (N = 9 and N = 1 respectively) compared well (root-mean-square error, RMSE < 0.80 cm) to manual estimates by independent observers (n = 3). The coefficient of multiple correlation (CMC) with manual estimates of fascicle length was comparable to previously reported for state-of-the-art optic flow algorithm (0.93-0.99), suggesting similar accuracy. The algorithm requires minimal manual intervention and can optionally extrapolate fascicle lengths that extend beyond the image frame. It facilitates automated analysis of ultrasound images without drift.
Dataset of the construction and characterization of stable biological nanoparticles
Authors: Gisonno Romina A. , Tricerri M. Alejandra , Gonzalez Marina C. , Garda Horacio A. , Ramella Nahuel A. , Ludovico Ivo Díaz 
Published: August 2020

AbstractWe suggest that the structural flexibility is key for certain proteins in order to fulfill functions that are required to interact with biological membranes, and that intra-chain chemical crosslinking may result in a different arrangement of protein with lipids. As interaction with biological membranes and lipids is a function attributed to many proteins in circulation, we intended to characterize an experimental design that helps in the study of many biological protein structures and their function. But in addition, by introducing intra-chain crosslinking, we obtained discoidal nano platforms that are stable under different conditions of temperate and time incubation. These platforms might be an excellent model to employ as biological carriers of intrinsic or external molecules. Thus, data shown here clearly strengthen the usefulness of an easy, accessible and inexpensive tool not only to study protein-lipid interactions, but to be used in different biological fields that require the transport of organic compounds.