bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colorimetric Test for Fast Detection of SARS-CoV-2 in Nasal and Throat Swabs
Authors: Della Ventura Bartolomeo , Cennamo Michele , Minopoli Antonio , Campanile Raffaele , Bolletti Censi Sergio , Terracciano Daniela , Portella Giuseppe , Velotta Raffaele 
Published: August 2020

AbstractMass testing is fundamental to face the pandemic caused by the coronavirus SARS-CoV-2 discovered at the end of 2019. To this aim, it is necessary to establish reliable, fast and cheap tools to detect viral particles in biological material so to identify the people capable to spread the infection. We demonstrate that a colorimetric biosensor based on gold nanoparticle (AuNP) interaction induced by SARS-CoV-2 lends itself as an outstanding tool for detecting viral particles in nasal and throat swabs. The extinction spectrum of a colloidal solution of multiple viral-target gold nanoparticles – AuNPs functionalized with antibodies targeting three surface proteins of SARS-CoV-2 (spike, envelope and membrane) – is redshifted in few minutes when mixed to a solution containing the viral particle. The optical density of the mixed solution measured at 560 nm was compared to the threshold cycle (Ct) of a Real Time-PCR (gold standard for detecting the presence of viruses) finding that the colorimetric method is able to detect very low viral load with a detection limit approaching that of RT-PCR. Since the method is sensitive to the infecting viral particle rather than to its RNA, the achievements reported here open new perspective not only in the context of the current and possible future pandemics, but also in microbiology as the biosensor proves itself to be a powerful though simple tool for measuring the viral particle concentration.
Mycobacterium tuberculosis whole genome sequence data support repurposing antileprosy antibiotic as antituberculosis
Authors: Saad Jamal , Gallou Jenny , Brieu Nathalie , Drancourt Michel , Baron Sophie Alexandra 
Published: August 2020

ABSTRACTBackgroundWe implanted WGS as the routine method to profile the antibiotic susceptibility of M. tuberculosis isolates focusing on in silico resistance to antileprosy drugs that we recently proposed to reposition for the treatment of pulmonary tuberculosis.MethodsWe prospectively performed WGS of 112 M. tuberculosis isolates recovered from respiratory tract samples of 106 patients diagnosed with pulmonary tuberculosis between 2017 and 2019 and defined their antibiotic susceptibility profile to 17 antibiotics including antileprotics drugs.ResultsWe incidentally observed 08 sequence variations in 07 genes, specific to seven sublineages. Altogether, we observed 09 (8%) rifampicin-resistant, 05 (4.4%) multidrug-resistant and 02 (1.7%) extensively-drug resistant isolates; whereas only one isolate exhibited in silico resistance to clofazimine.ConclusionThese results support repurposing of antileprosis antibiotics as antituberculosis; and offer new targets for genotyping M. tuberculosis.
Study of Coronavirus Impact on Parisian Population from April to June using Twitter and Text Mining Approach
Authors: Chire Saire Josimar E. , Cruz Jimy Frank Oblitas 
Published: August 2020

AbstractThe fast spreading of coronavirus name covid19, generated the actual pandemic forcing to change daily activities. Health Councils of each country promote health policies, close borders and start a partial or total lockdown. One of the first countries in Europe with high impact was Italy. Besides at the end of April, one country with a shared border was on the top of 10 countries with more total cases, then France started with its own battle to beat coronavirus. This paper studies the impact of coronavirus in the poopulation of Paris, France from April 23 to June 18, using Text Mining approach, processing data collected from Social Network and using trends related of searching. First finding is a decreasing pattern of publications/interest, and second is related to health crisis and economical impact generated by coronavirus.
Invasion performance-similarity found among multiple cell systems
Authors: Prakash Om 
Published: August 2020

ABSTRACTUnderstanding of inter-system behavior develops biologically relevant intuition for drug repositioning as well as other biological research. But combining all the possible genes interactions into a system, and furthermore comparisons of multiple systems are a challenge on time ground with feasible experiments. In present study, 64 cell lines from 11 different organs were compared for their invasion performance. RNA expressions of 23 genes were used to create systems artificial neural network (ANN) models. ANN models were prepared for all 64 cell lines and observed for their invasion performance through network mapping. The resulted cell line clusters bear feasible capacity to perform experiments for biologically relevant research motivations as drug repositioning and selective targeting etc.; and can be used for analysis of invasion related aspects.
Abnormal Upregulation of Cardiovascular Disease Biomarker PLA2G7 Induced by Proinflammatory Macrophages in COVID-19 patients
Authors: Li Yang , Jiang Yongzhong , Zhang Yi , Li Naizhe , Yin Qiangling , Liu Linlin , Lv Xin , Liu Yan , Li Aqian , Fang Bin , Li Jiajia , Ye Hengping , Yang Gang , Cui Xiaoxian , Liu Yang , Qu Yuanyuan , Li Chuan , Li Jiandong , Li Dexin , Wang Shiwen , Gai Zhongtao , Zhan Faxian , Liang Mifang 
Published: August 2020

AbstractBACKGROUNDCoronavirus disease 2019 (COVID-19) triggers distinct patterns of pneumonia progression with multiorgan disease, calling for cell- and/or tissue-type specific host injury markers.METHODSAn integrated hypothesis-free single biomarker analysis framework was performed on nasal swabs (n = 484) from patients with COVID-19 in GSE152075. The origin of candidate biomarker was assessed in single-cell RNA data (GSE145926). The candidate biomarker was validated in a cross-sectional cohort (n = 564) at both nucleotide and protein levels.RESULTSPhospholipase A2 group VII (PLA2G7) was identified as a candidate biomarker in COVID-19. PLA2G7 was predominantly expressed by proinflammatory macrophages in lungs emerging with progression of COVID-19. In the validation stage, PLA2G7 was found in patients with COVID-19 and pneumonia, especially in severe pneumonia, rather than patients suffered mild H1N1 influenza infection. Up to 100% positive rates of PLA2G7 were positively correlated with not only viral loads in patients with COVID-19 but also severity of pneumonia in non-COVID-19 patients. Although Ct values of PLA2G7 in severe pneumonia was significantly lower than that in moderate pneumonia (P = 7.2e-11), no differences were observed in moderate pneumonia with COVID-19 between severe pneumonia without COVID-19 (P = 0.81). Serum protein levels of PLA2G7, also known as lipoprotein-associated phospholipase A2 (Lp-PLA2), were further found to be elevated and beyond the upper limit of normal in patients with COVID-19, especially among the re-positive patients.CONCLUSIONSWe firstly identified and validated PLA2G7, a biomarker for cardiovascular diseases (CVDs), was abnormally enhanced in COVID-19 patients at both nucleotide and protein aspects. These findings provided indications into the prevalence of cardiovascular involvements seen in COVID-19 patients. PLA2G7 could be a hallmark of COVID-19 for monitoring disease progress and therapeutic response.FUNDINGThis study was supported by grants from China Mega-Projects for Infectious Disease (2018ZX10711001), National Natural Science Foundation of China (82041023).
Quantifying the efficiency of non-pharmaceutical interventions against SARS-COV-2 transmission in Europe
Authors: garchitorena Andres , Gruson Hugo , Cazelles Bernard , Roche Benjamin 
Published: August 2020

AbstractSince the emergence of SARS-CoV-2, governments around the World have implemented a combination of public health responses based on non-pharmaceutical interventions (NPIs), with significant social and economic consequences. Though most European countries have overcome the first epidemic wave, it remains of high priority to quantify the efficiency of different NPIs to inform preparedness for an impending second wave. In this study, combining capture-recapture methods with Bayesian inference in an age-structured mathematical model, we use a unique European dataset compiled by the European Centre for Disease Control (ECDC) to quantify the efficiency of 24 NPIs and their combinations (referred to as public health responses, PHR) in reducing SARS-Cov-2 transmission rates in 32 European countries. Of 166 unique PHR tested, we found that median decrease in viral transmission was 74%, which is enough to suppress the epidemic. PHR efficiency was positively associated with the number of NPIs implemented. We found that bans on mass gatherings had the largest effect among NPIs, followed by school closures, teleworking, and stay home orders. Partial implementation of most NPIs resulted in lower than average response efficiency. This first large-scale estimation of NPI and PHR efficiency against SARS-COV-2 transmission in Europe suggests that a combination of NPIs targeting different population groups should be favored to control future epidemic waves.
Evolving Virulence? Decreasing COVID-19 Complications among Massachusetts Healthcare Workers: A Cohort Study
Authors: Lan Fan-Yun , Filler Robert , Mathew Soni , Iliaki Eirini , Osgood Rebecca , Bruno-Murtha Lou Ann , Kales Stefanos N. 
Published: August 2020

AbstractThe hypothesis of attenuating SARS-CoV-2 virulence has been raised. We examined the temporal distribution of COVID-19 complications (ER visits, hospitalization, intubation/code, and/or death) among healthcare workers in one system that applied uniform screening criteria throughout the research period, and found the complication rate significantly decreased after April 15, 2020.
MORPHIOUS: A Machine Learning Workflow to Naively Detect the Activation of Microglia and Astrocytes
Authors: Silburt Joseph , Aubert Isabelle 
Published: August 2020

AbstractIn cases of brain injury, degeneration and repair, defining microglia and astrocytic activation using cellular markers alone remains a challenging task. We developed MORPHIOUS, an unsupervised machine learning workflow that utilizes a one-class support vector machine to segment clusters of activated glia by only referencing examples of non-activated glia. Here, glial activation was triggered using focused ultrasound to permeabilize the hippocampal blood-brain barrier. Analyzing the hippocampal sections seven days later, MORPHIOUS identified two classes of microglia which showed characteristic activation features, including increases in ionized calcium-binding adapter molecule 1 expression, soma size, and de-ramification. MORPHIOUS was further used to identify clusters of activated astrocytes, which showed increased expression of glial fibrillary acidic protein and branching. Thus, by only referencing untreated glia morphologies, MORPHIOUS can identify diverse and novel manifestations of glial activation. This provides significant improvements for characterizing glial activation in cases of injury, neurodegeneration, and regeneration.
Learning can be detrimental for a parasitic wasp
Authors: Bertoldi Valeria , Rondoni Gabriele , Peri Ezio , Conti Eric , Brodeur Jacques 
Published: August 2020

AbstractAnimals have evolved the capacity to learn, and the conventional view is that learning allows individuals to improve foraging decisions. We describe a first case of maladaptive learning where a parasitoid learns to associate chemical cues from an unsuitable host, thereby re-enforcing a reproductive cul-de-sac (evolutionary trap).Telenomus podisiparasitizes eggs of the exotic stink bugHalyomorpha halysat the same rate as eggs of its coevolved host,Podisus maculiventris, but the parasitoid cannot complete its development in the exotic species. We hypothesized thatT. podisilearns to exploit cues from this non-coevolved species, thereby increasing unsuccessful parasitism rates. We conducted bioassays to compare the responses of naïvevs. experienced parasitoids on chemical footprints left by one of the two host species. Both naïve and experienced females showed a higher response to footprints ofP. maculiventristhan ofH. halys. Furthermore, parasitoids that gained an experience onH. halyssignificantly increased their residence time within the arena and the frequency of re-encounter with the area contaminated by chemical cues. Maladaptive learning in theT. podisi-H. halysassociation is expected to further decrease parasitoid reproductive success and have consequences for population dynamics of sympatric native and exotic host species.
Consequences of the divergence of Methionine AdenosylTransferase
Authors: Chouhan Bhanupratap Singh , Gade Madhuri H. , Martinez Desirae , Toledo-Patino Saacnicteh , Laurino Paola 
Published: August 2020

AbstractMethionine adenosyltransferase (MAT), which catalyzes the biosynthesis of S-adenosylmethionine from L-methionine and ATP, is an ancient, highly conserved enzyme present in all three domains of life. Although the MAT enzymes of each domain are believed to share a common ancestor, the sequences of archaeal MATs show a high degree of divergence from the sequences of bacterial and eukaryotic MATs. However, the structural and functional consequences of this sequence divergence are not well understood. Here, we use structural bioinformatics analysis and ancestral sequence reconstruction to highlight the consequences of archaeal MAT divergence. We show that the dimer interface containing the active site, which would be expected to be well conserved across all three domains, diverged considerably between the bacterial/eukaryotic MATs and archaeal MATs. Furthermore, the characterization of reconstructed ancestral archaeal MATs showed that they probably had low substrate specificity which expanded during their evolutionary trajectory hinting towards the observation that all the modern day MAT enzymes from the three-kingdom probably originated from a common specific ancestor and then archaea MATs diverged in sequence, structure and substrate specificity. Altogether, our results show that the archaea MAT is an ideal system for studying an enzyme family which evolved to display high degrees of divergence at the sequence/structural levels and yet are capable of performing the same catalytic reactions as their orthologous counterparts.
In vivo Restricted-Diffusion Imaging (RDI) is sensitive to differences in axonal density in typical children and adults
Authors: Garic Dea , Yeh Fang-Cheng , Graziano Paulo , Dick Anthony Steven 
Published: August 2020

ABSTRACTBackgroundThe ability to dissociate axonal densityin vivofrom other microstructural properties of white matter is important for the diagnosis and treatment of neurologic disease, and new methods to do so are being developed. We investigated one such method–restricted diffusion imaging (RDI)–to see whether it can more accurately replicate histological axonal density patterns in the corpus callosum (CC) of adults and children compared to diffusion tensor imaging (DTI), neurite orientation dispersion and density imaging (NODDI), and generalized q-sampling imaging (GQI) methods. To do so, we compared known axonal density patterns defined by histology to to diffusion-weighted imaging (DWI) scans of 840 healthy 20- to 40-year-old adults, and, in a replication and extension, to DWI scans of 129 typically developing 7-month-old to 18-year-old children and adolescents. Contrast analyses were used to to compare pattern similarities between thein-vivometric and previously-published histological density models. We found that RDI was effective at mapping axonal density of small (Cohen’sd= 2.60) and large fiber sizes (Cohen’sd= 2.84) in adults. The same pattern was observed in the developing sample (Cohen’sd= 3.09 and 3.78, respectively). Other metrics, notably NODDI’s intracellular volume fraction (ICVF), were also sensitive to differences in axonal density across the longitudinal axis of the CC. In conclusion, the study showed that RDI is effective at measuring axonal density of small and large axons in adults and children, with both single- and multi-shell acquisition DWI data. Its effectiveness and availability to be used on standard as well as advanced DWI acquisitions makes it a promising method in clinical settings.
The Temporal Statistics of Musical Rhythm across Western Genres: An Amplitude Modulation Phase Hierarchy Model
Authors: Daikoku Tatsuya , Goswami Usha 
Published: August 2020

AbstractStatistical learning by the human brain plays a core role in the development of cognitive systems like language and music. Both music and speech have structured inherent rhythms, however the acoustic sources of these rhythms are debated. Theoretically, rhythm structures in both systems may be related to a novel set of acoustic statistics embedded in the amplitude envelope, statistics originally revealed by modelling children’s nursery rhymes. Here we apply similar modelling to explore whether the amplitude modulation (AM) timescales underlying rhythm in music match those in child-directed speech (CDS). Utilising AM-driven phase hierarchy modelling previously applied to infant-directed speech (IDS), adult-directed speech (ADS) and CDS, we test whether the physical stimulus characteristics that yield speech rhythm in IDS and CDS describe rhythm in music. Two models were applied. One utilized a low-dimensional representation of the auditory signal adjusted for known mechanisms of the human cochlear, and the second utilized probabilistic amplitude demodulation, estimating the modulator (envelope) and carriers using Bayesian inference. Both models revealed a similar hierarchically-nested temporal modulation structure across Western musical genres and instruments. Core bands of AM and spectral patterning matched prior analyses of IDS and CDS, and music showed strong phase dependence between slower bands of AMs, again matching IDS and CDS. This phase dependence is critical to the perception of rhythm. Control analyses modelling other natural sounds (wind, rain, storms, rivers) did not show similar temporal modulation structures and phase dependencies. We conclude that acoustic rhythm in language and music has a shared statistical basis.
Automated improvement of stickleback reference genome assemblies with Lep-Anchor software
Authors: Kivikoski Mikko , Rastas Pasi , Löytynoja Ari , Merilä Juha 
Published: August 2020

SummaryWe describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.7 Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.
PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction
Authors: Liu Yuanlong , Teng Chong , Xia Rui , Meyers Blake C. 
Published: August 2020

AbstractPhased secondary small interfering RNAs (phasiRNAs) constitute a major category of small RNAs in plants, but most of their functions are still poorly defined. Some phasiRNAs, known as trans-acting siRNAs, are known to target complementary mRNAs for degradation and to function in development. However, the targets or biological roles of other phasiRNAs remain speculative. New insights into phasiRNA biogenesis, their conservation, and their variation across the flowering plants continue to emerge due to the increased availability of plant genomic sequences, deeper and more sophisticated sequencing approaches, and improvements in computational biology and biochemical/molecular/genetic analyses. In this review, we survey recent progress in phasiRNA biology, with a particular focus on two classes associated with male reproduction: 21-nucleotide (accumulate early in anther ontogeny) and 24-nucloetide (produced in somatic cells during meiosis) phasiRNAs. We describe phasiRNA biogenesis, function, and evolution and define the unanswered questions that represent topics for future research.
Roles of gender and basic need satisfaction in decent work perception and voice behavior
Authors: Huang Wenyuan , Shen Jie , Yuan Chuqin , Li Min 
Published: August 2020

PurposeHow to foster voice behavior has always been a hot topic in organizational research; however, the mechanism through which performing decent work affects employee voice behavior remains to be fully understood. To address this deficiency, the current study investigates how basic need satisfaction may relate to perceived decent work and voice behavior and the moderating role of gender. Our research draws upon self-determination theory and social information processing theory.Design/methodology/approachThe theoretical model was tested using two-wave investigation data collected from a sample of 349 employees and 85 supervisors in Southwest China.FindingsDecent work perception was positively related to voice behavior, and this relationship was partially mediated by basic need satisfaction. In addition, the relationship between decent work perception and basic need satisfaction as well as the indirect effect of decent work perception on voice behavior via basic need satisfaction was stronger for men than for women.Originality/valueThis study highlights the pivotal roles of basic need satisfaction and gender in the consequences of decent work perception in the workplace. The authors provide new insights into the relationship between decent work perception and voice behavior and inspire scholars to elucidate other explanatory mechanisms in this link.
Students' perceptions regarding classroom attendance and its impact on their academic performance: evidence from a developing country
Authors: Almutawa Abdullah , Suwaidan Mishiel Said 
Published: August 2020

PurposeThe purposes of this study are to identify the reasons that prevent students from attending lectures, to examine the impact of absenteeism on their academic performance and to explore the role of gender in their attendance.Design/methodology/approachA questionnaire survey made up of statements was distributed to accounting students. Descriptive measures, a five-point Likert scale, Pearson's chi-square test and phi test were employed to achieve the study's objectives.FindingsThe study shows that most of the accounting students surveyed are aware of the importance of attending lectures, since they believe that attendance will have a positive impact on their understanding of course material and on their academic performance. The study indicates that overall academic performance and student attendance are related. It also indicates that there is a statistically significant association between the overall academic performance of accounting students and their gender.Practical implicationsTo gain greater insight into educators, academic institutes, researchers and parents concerning the reasons that lie behind students not attending accounting lectures in public higher education institutions in Kuwait and the effect of attendance on academic performance.Originality/valueMost prior studies have been conducted in developed countries and Western contexts. Especially, with the potential perceived differences in cultures and norms, this empirical study is expected to contribute to fill the gap in this research field.