An Empirical Methodology for Detecting and Prioritizing Needs during Crisis Events

In times of crisis, identifying the essential needs is a crucial step to providing appropriate resources and services to affected entities. Social media platforms such as Twitter contain vast amount of information about the general public's needs. However, the sparsity of the information as well as the amount of noisy content present a challenge to practitioners to effectively identify shared information on these platforms. In this study, we propose two novel methods for two distinct but related needs detection tasks: the identification of 1) a list of resources needed ranked by priority, and 2) sentences that specify who-needs-what resources. We evaluated our methods on a set of tweets about the COVID-19 crisis. For task 1 (detecting top needs), we compared our results against two given lists of resources and achieved 64% precision. For task 2 (detecting who-needs-what), we compared our results on a set of 1,000 annotated tweets and achieved a 68% F1-score

Antimicrobial activity of spherical silver nanoparticles prepared using a biocompatible macromolecular capping agent: evidence for induction of a greatly prolonged bacterial lag phase

<p>Abstract</p> <p>Background</p> <p>We have evaluated the antimicrobial properties of Ag-based nanoparticles (<it>Np</it>s) using two solid phase bioassays and found that 10-20 μL of 0.3-3 μM keratin-stabilized <it>Np</it>s (depending on the starting bacterial concentration = <it>C</it>_I) completely inhibited the growth of an equivalent volume of <it>ca</it>. 10³to 10⁴colony forming units per mL (CFU mL^-1) <it>Staphylococcus aureus</it>, <it>Salmonella </it>Typhimurium, or <it>Escherichia coli </it>O157:H7 on solid surfaces. Even after one week at 37°C on solid media, no growth was observed. At lower <it>Np </it>concentrations (= [<it>Np</it>]s), visible colonies were observed but they eventually ceased growing.</p> <p>Results</p> <p>To further study the physiology of this growth inhibition, we repeated these experiments in liquid phase by observing microbial growth via optical density at 590 nm (OD) at 37°C in the presence of a [<it>Np</it>] = 0 to 10^-6M. To extract various growth parameters we fit all OD[t] data to a common sigmoidal function which provides measures of the beginning and final OD values, a first-order rate constant (<it>k</it>), as well as the time to calculated 1/2-maximal OD (<it>t</it>_m) which is a function of <it>C</it>_I, <it>k</it>, as well as the microbiological lag time (<it>T</it>).</p> <p>Performing such experiments using a 96-well microtitre plate reader, we found that growth <it>always </it>occurred in solution but <it>t</it>_mvaried between 7 (controls; <it>C</it>_I= 8 × 10³CFU mL^-1) and > 20 hrs using either the citrate-([<it>Np</it>] ~ 3 × 10^-7M) or keratin-based ([<it>Np</it>] ~ 10^-6M) <it>Np</it>s and observed that {∂<it>t</it>_m/∂ [<it>Np</it>]}_citrate~ 5 × 10⁷and {∂<it>t</it>_m/∂ [<it>Np</it>]}_keratin~ 10⁷hr·L mol^-1. We also found that there was little effect of <it>Np</it>s on <it>S. aureus </it>growth rates which varied only between <it>k </it>= 1.0 and 1.2 hr^-1(1.1 ± 0.075 hr^-1). To test the idea that the <it>Np</it>s were changing the initial concentration (<it>C</it>_I) of bacteria (<it>i.e</it>., cell death), we performed probabilistic calculations assuming that the perturbations in <it>t</it>_mwere due to <it>C</it>_Ialone. We found that such large perturbations in <it>t</it>_mcould only come about at a <it>C</it>_Iwhere the probability of any growth at all was small. This result indicates that much of the <it>Np</it>-induced change in <it>t</it>_mwas due to a greatly increased <it>T </it>(<it>e.g</it>., from <it>ca</it>. 1 to 15-20 hrs). For the solid phase assays we hypothesize that the bacteria eventually became non-culturable since they were inhibited from undergoing further cell division (<it>T </it>> many days).</p> <p>Conclusion</p> <p>We propose that the difference between the solid and liquid system relates to the obvious difference in the exposure, or residence, time of the <it>Np</it>s with respect to the bacterial cell membrane inasmuch as when small, <it>Np</it>-inhibited colonies were selected and streaked on fresh (<it>i.e</it>., no <it>Np</it>s present) media, growth proceeded normally: <it>e.g</it>., a small, growth-inhibited colony resulted in a plateful of typical <it>S. aureus </it>colonies when streaked on fresh, solid media.</p

Natural co-infection of influenza A/H3N2 and A/H1N1pdm09 viruses resulting in a reassortant A/H3N2 virus

Background: Despite annual co-circulation of different subtypes of seasonal influenza, co-infections between different viruses are rarely detected. These co-infections can result in the emergence of reassortant progeny. Study design: We document the detection of an influenza co-infection, between influenza A/H3N2 with A/H1N1pdm09 viruses, which occurred in a 3 year old male in Cambodia during April 2014. Both viruses were detected in the patient at relatively high viral loads (as determined by real-time RT-PCR CT values), which is unusual for influenza co-infections. As reassortment can occur between co-infected influenza A strains we isolated plaque purified clonal viral populations from the clinical material of the patient infected with A/H3N2 and A/H1N1pdm09. Results: Complete genome sequences were completed for 7 clonal viruses to determine if any reassorted viruses were generated during the influenza virus co-infection. Although most of the viral sequences were consistent with wild-type A/H3N2 or A/H1N1pdm09, one reassortant A/H3N2 virus was isolated which contained an A/H1N1pdm09 NS1 gene fragment. The reassortant virus was viable and able to infect cells, as judged by successful passage in MDCK cells, achieving a TCID50 of 104/ml at passage number two. There is no evidence that the reassortant virus was transmitted further. The co-infection occurred during a period when co-circulation of A/H3N2 and A/H1N1pdm09 was detected in Cambodia. Conclusions: It is unclear how often influenza co-infections occur, but laboratories should consider influenza co-infections during routine surveillance activities

Establishing seasonal and alert influenza thresholds in Cambodia using the WHO method: implications for effective utilization of influenza surveillance in the tropics and subtropics

Objective: To establish seasonal and alert thresholds and transmission intensity categories for influenza to provide timely triggers for preventive measures or upscaling control measures in Cambodia. Methods: Using Cambodia's influenza-like illness (ILI) and laboratory-confirmed influenza surveillance data from 2009 to 2015, three parameters were assessed to monitor influenza activity: the proportion of ILI patients among all outpatients, proportion of ILI samples positive for influenza and the product of the two. With these parameters, four threshold levels (seasonal, moderate, high and alert) were established and transmission intensity was categorized based on a World Health Organization alignment method. Parameters were compared against their respective thresholds. Results: Distinct seasonality was observed using the two parameters that incorporated laboratory data. Thresholds established using the composite parameter, combining syndromic and laboratory data, had the least number of false alarms in declaring season onset and were most useful in monitoring intensity. Unlike in temperate regions, the syndromic parameter was less useful in monitoring influenza activity or for setting thresholds. Conclusion: Influenza thresholds based on appropriate parameters have the potential to provide timely triggers for public health measures in a tropical country where monitoring and assessing influenza activity has been challenging. Based on these findings, the Ministry of Health plans to raise general awareness regarding influenza among the medical community and the general public. Our findings have important implications for countries in the tropics/subtropics and in resource-limited settings, and categorized transmission intensity can be used to assess severity of potential pandemic influenza as well as seasonal influenza

Circulation and characterization of seasonal influenza viruses in Cambodia, 2012‐2015

Background: Influenza virus circulation is monitored through the Cambodian influenza‐like illness (ILI) sentinel surveillance system and isolates are characterized by the National Influenza Centre (NIC). Seasonal influenza circulation has previously been characterized by year‐round activity and a peak during the rainy season (June‐November). Objectives: We documented the circulation of seasonal influenza in Cambodia for 2012‐2015 and investigated genetic, antigenic, and antiviral resistance characteristics of influenza isolates. Patients/Methods Respiratory samples were collected from patients presenting with influenza‐like illness (ILI) at 11 hospitals throughout Cambodia. First‐line screening was conducted by the National Institute of Public Health and the Armed Forces Research Institute of Medical Sciences. Confirmation of testing and genetic, antigenic and antiviral resistance characterization was conducted by Institute Pasteur in Cambodia, the NIC. Additional virus characterization was conducted by the WHO Collaborating Centre for Reference and Research on Influenza (Melbourne, Australia). Results: Between 2012 and 2015, 1,238 influenza‐positive samples were submitted to the NIC. Influenza A(H3N2) (55.3%) was the dominant subtype, followed by influenza B (30.9%; predominantly B/Yamagata‐lineage) and A(H1N1)pdm09 (13.9%). Circulation of influenza viruses began earlier in 2014 and 2015 than previously described, coincident with the emergence of A(H3N2) clades 3C.2a and 3C.3a, respectively. There was high diversity in the antigenicity of A(H3N2) viruses, and to a smaller extent influenza B viruses, during this period, with some mismatches with the northern and southern hemisphere vaccine formulations. All isolates tested were susceptible to the influenza antiviral drugs oseltamivir and zanamivir. Conclusions: Seasonal and year‐round co‐circulation of multiple influenza types/subtypes were detected in Cambodia during 2012‐2015

Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation

During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual.In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively.These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation

Evidence for a bimodal distribution of Escherichia coli doubling times below a threshold initial cell concentration

Abstract Background In the process of developing a microplate-based growth assay, we discovered that our test organism, a native E. coli isolate, displayed very uniform doubling times (τ) only up to a certain threshold cell density. Below this cell concentration (≤ 100 -1,000 CFU mL-1 ; ≤ 27-270 CFU well-1) we observed an obvious increase in the τ scatter. Results Working with a food-borne E. coli isolate we found that τ values derived from two different microtiter platereader-based techniques (i.e., optical density with growth time {=OD[t]} fit to the sigmoidal Boltzmann equation or time to calculated 1/2-maximal OD {=tm} as a function of initial cell density {=tm[CI]}) were in excellent agreement with the same parameter acquired from total aerobic plate counting. Thus, using either Luria-Bertani (LB) or defined (MM) media at 37°C, τ ranged between 17-18 (LB) or 51-54 (MM) min. Making use of such OD[t] data we collected many observations of τ as a function of manifold initial or starting cell concentrations (CI). We noticed that τ appeared to be distributed in two populations (bimodal) at low CI. When CI ≤100 CFU mL-1 (stationary phase cells in LB), we found that about 48% of the observed τ values were normally distributed around a mean (μτ1) of 18 ± 0.68 min (± στ1) and 52% with μτ2 = 20 ± 2.5 min (n = 479). However, at higher starting cell densities (CI>100 CFU mL-1), the τ values were distributed unimodally (μτ = 18 ± 0.71 min; n = 174). Inclusion of a small amount of ethyl acetate to the LB caused a collapse of the bimodal to a unimodal form. Comparable bimodal τ distribution results were also observed using E. coli cells diluted from mid-log phase cultures. Similar results were also obtained when using either an E. coli O157:H7 or a Citrobacter strain. When sterile-filtered LB supernatants, which formerly contained relatively low concentrations of bacteria(1,000-10,000 CFU mL-1), were employed as a diluent, there was an evident shift of the two populations towards each other but the bimodal effect was still apparent using either stationary or log phase cells. Conclusion These data argue that there is a dependence of growth rate on starting cell density.</p

Performance Analysis of Orthogonal Pairs Designed for an Expanded Eukaryotic Genetic Code

Background: The suppression of amber stop codons with non-canonical amino acids (ncAAs) is used for the site-specific introduction of many unusual functions into proteins. Specific orthogonal aminoacyl-tRNA synthetase (o-aaRS)/amber suppressor tRNA CUA pairs (o-pairs) for the incorporation of ncAAs in S. cerevisiae were previously selected from an E. coli tyrosyl-tRNA synthetase/tRNACUA mutant library. Incorporation fidelity relies on the specificity of the o-aaRSs for their ncAAs and the ability to effectively discriminate against their natural substrate Tyr or any other canonical amino acid. Methodology/Principal Findings: We used o-pairs previously developed for ncAAs carrying reactive alkyne-, azido-, or photocrosslinker side chains to suppress an amber mutant of human superoxide dismutase 1 in S. cerevisiae. We found worse incorporation efficiencies of the alkyne- and the photocrosslinker ncAAs than reported earlier. In our hands, amber suppression with the ncAA containing the azido group did not occur at all. In addition to the incorporation experiments in S. cerevisiae, we analyzed the catalytic properties of the o-aaRSs in vitro. Surprisingly, all o-aaRSs showed much higher preference for their natural substrate Tyr than for any of the tested ncAAs. While it is unclear why efficiently recognized Tyr is not inserted at amber codons, we speculate that metabolically inert ncAAs accumulate in the cell, and for this reason they are incorporated despite being weak substrates for the o-aaRSs. Conclusions/Significance: O-pairs have been developed for a whole plethora of ncAAs. However, a systematic and detaile

A Long Road for Stem Cells to Cure Sick Hearts: Update on Recent Clinical Trials

The contribution of stem cells to cure damaged hearts has finally been unraveled. A large number of preclinical and clinical studies have showed beneficial outcomes after myocardial infarction. In this review, the current understanding of stem cell therapy in preclinical and clinical experiences is summarized. Stem cells from bone marrow have shown a potential to improve cardiac performance after myocardial infarction in animal and early clinical studies. Clinical trials from all over the world have provided safety assessments of stem cell therapy with marginal improvement of clinical outcomes. Thus, further investigations should be encouraged to resolve the discrepancies between studies, clinical issues, and unclear translational findings. This review provides information and commentary on key trials for stem cell-based treat-ment of cardiovascular disease