Modelling the flow and mass transport in canopies requires knowledge of how roughness heterogeneity impacts them. We present wind-tunnel experiments that enable quantifying the (time-space) average flow statistics of a two-height model canopy. We use two-dimensional particle image velocimetry measurements of the flow in multiple planes inside the canopy layer (CL), the roughness sublayer, and above it. The canopy comprises thin metal plates of two heights, h and h/2, which form a specific heterogeneity that can be viewed as two horizontal layers, “top” and “bottom”. The overall frontal index (\(\lambda =0.5\)) resides in a less-studied dynamical zone between “dense” (\(> 0.5\)) and “sparse” (\(0.1<\lambda < 0.5\)). The effects of the canopy’s heterogeneity are highlighted by comparing the flow statistics, with published results from dense and sparse uniform canopies made of similar element shapes. The plane mixing layer analogy was reflected in the first-, second-, and third-order moments of the velocity fluctuations, as well as in the quadrant analysis of the Reynolds shear stress, with few reservations: (i) the shear length scale at canopy height, which quantifies the inverse of the mean shear, is relatively smaller than would have been expected from the momentum penetration depth \(h-d\); (ii) An additional inflection point, obeying the inviscid Fjørtoft’s criterion, is observed in the average streamwise velocity at the bottom-layer height (h/2), where a local increase in sweep/ejection events of the Reynolds shear stress are prominent; (iii) unlike typical dense canopies, the estimated contribution from wake to the production of TKE near the top CL is smaller relative to the contributions from shear; (iv) the dispersive fluxes of the shear stress and kinetic energy differ from that of uniform canopies that are either denser or sparser. These observations provide new insights into the possible impact that vertical roughness heterogeneity has on the flow statistics in plant and urban canopies.

Monkeypox virus (MPXV) resides in two forms; mature and enveloped, and depending on it, distinct proteins are displayed on the viral surface. Here, we expressed two MPXV antigens from the mature, and one from the enveloped form, and tested their reactivity to sera of 11 MPXV recoverees while comparing to sera from recently and past vaccinated individuals. 8 out of 11 recoverees exhibited detectable neutralization levels against Vaccinia Lister. Sera from all recoverees bound strongly to A35R and H3L antigens. Moreover, the responses to A35R were significantly higher within the recoverees compared to both recently and past vaccinated donors. Lastly, A35R- and H3L-specific IgG⁺ B cells ranging from 0.03-0.46% and 0.11–0.36%, respectively, were detected in all recoverees (A35R), and in 9 out of 11 recoverees (H3L). Therefore, A35R and H3L represent MPXV immune targets and could be used in a heat-inactivated serological ELISA for the identification of recent MPXV infection.

Chemical analysis of hazardous surface contaminations, such as hazardous substances, explosives or illicit drugs, is an essential task in security, environmental and safety applications. This task is mostly based on the collection of particles with swabs, followed by thermal desorption into a vapor analyzer, usually a detector based on ion mobility spectrometry (IMS). While this methodology is well established for several civil applications, such as border control, it is still not efficient enough for various conditions, as in sampling rough and porous surfaces. Additionally, the process of thermal desorption is energetically inefficient, requires bulky hardware and introduces device contamination memory effects. Low-temperature plasma (LTP) has been demonstrated as an ionization and desorption source for sample preparation-free analysis, mostly at the inlet of a mass spectrometer analyzer, and in rare cases in conjunction with an ion mobility spectrometer. Herein, we demonstrate, for the first time, the operation of a simple, low cost, home-built LTP apparatus for desorbing non-volatile analytes from various porous surfaces into the inlet of a handheld IMS vapor analyzer. We show ion mobility spectra that originate from operating the LTP jet on porous surfaces such as asphalt and shoes, contaminated with model amine-containing organic compounds. The spectra are in good correlation with spectra measured for thermally desorbed species. We verify through LC-MS analysis of the collected vapors that the sampled species are not fragmented, and can thus be identified by commercial IMS detectors.

Bacillus anthracis overcomes host immune responses by producing capsule and secreting toxins. Production of these virulence factors in response to entering the host environment was shown to be regulated by atxA, the major virulence regulator, known to be activated by HCO3- and CO2. While toxin production is regulated directly by atxA, capsule production is independently mediated by two regulators; acpA and acpB. In addition, it was demonstrated that acpA has at least two promotors, one of them shared with atxA. We used a genetic approach to study capsule and toxin production under different conditions. Unlike previous works utilizing NBY, CA or R-HCO3- medium under CO2 enriched conditions, we used a sDMEM-based medium. Thus, toxin and capsule production can be induced in ambient or CO2 enriched atmosphere. Using this system, we could differentiate between induction by 10% NRS, 10% CO2 or 0.75% HCO3-. In response to high CO2, capsule production is induced by acpA based response in an atxA-independent manner, with little to no toxin (protective antigen PA) production. atxA based response is activated in response to serum independently of CO2, inducing toxin and capsule production in an acpA or acpB dependent manner. HCO3- was also found to activate atxA based response, but in non-physiological concentrations. Our findings may help explain the first stages of inhalational infection, in which spores germinating in dendritic cells require protection (by encapsulation) without affecting cell migration to the draining lymph-node by toxin secretion.

Information and decision support systems are essential to conducting field campaigns in the atmospheric sciences. However, their development is costly and time-consuming since each field campaign has its own research goals, which result in using an assortment of sensors and various analysis procedures. To reduce development costs, we present a software framework based on the Industrial Internet of Things (IIOT) and an implementation using well-established and newly developed open-source components. This framework architecture and components allow developers to customize the software to a campaign's specific needs while keeping the coding minimum. Using this framework, we developed an Information and decision support system for an indoor dispersion campaign.

Sulfur mustard (SM)-induced ocular injury is characterized by an acute inflammatory response that may become chronic or enter a latent phase with delayed pathology. This study aimed to evaluate the efficacy of ziv-aflibercept and aflibercept in preventing and ameliorating corneal neovascularization (NV), respectively, following chemical eye exposure to SM vapor in a rabbit model. Chemical SM ocular insult was induced in the right eye of rabbits. A single application of ziv-aflibercept was administered 2 h or 9 days post-exposure. A single subconjunctival aflibercept treatment in an ocular formulation was administered 4 weeks after SM vapor exposure and subsequent to an initial 1-week treatment with 0.1 % dexamethasone. Clinical monitoring was performed 5–12 weeks post-exposure, and digital corneal pictures were taken to assess the extent of NV. The rabbits were euthanized and the corneas were processed for histological assessment. Treatment with ziv-aflibercept 2 h and 9 days post-exposure moderately reduced insult severity and partially delayed or prevented corneal NV. Aflibercept application 4 weeks post-exposure significantly reduced the extent of NV for 8 weeks. The substantial decrease in existing corneal NV in this group was confirmed by histology. These results reveal the powerful anti-angiogenic efficacy of the VEGF-trap for ameliorating existing NV as opposed to preventing NV development, revealing the ability of this treatment to mitigate corneal NV.

Microbial adaptation to changing environmental conditions is frequently mediated by hypermutable sequences. Here we show that such a hypermutable hotspot within a gene encoding a flagellar unit of Paenibacillus glucanolyticus, generated spontaneous non-swarming mutants with increased stress resistance. These mutants, which survived conditions that eliminated wild-type cultures, could be carried by their swarming siblings when the colony spread, consequently increasing their numbers at the spreading edge. Interestingly, the hypermutable nature of the aforementioned sequence enabled the non-swarming mutants to serve as “seeds” for a new generation of wild-type cells through reversion of the mutation. Using a mathematical model, we examined the survival dynamics of P. glucanolyticus colonies under fluctuating environments. Our experimental and theoretical results suggest that the non-swarming, stress-resistant mutants can save the colony from extinction. Notably, we identified this hypermutable sequence in flagellar genes of additional Paenibacillus species, suggesting that this phenomenon could be wide-spread and ecologically important.

Analytical chemists are often challenged to screen for bioactive compounds in complex matrices, sometimes without a priori knowledge of the exact compound of interest. Therefore, “flagging” techniques, highlighting common characteristics of bioactive compounds, are highly sought after. In this work, we demonstrate a double flagging method, where unknown organophosphorus acetylcholinesterase inhibitors are “flagged” out of a complex matrix by the presence of organophosphorus-indicative ions as well as their acetylcholinesterase inhibition. This is accomplished by flagging the LC chromatographic retention time of phosphorus-indicative ions using accurate mass high-energy in-source CID products, and the retention time of acetylcholinesterase inhibiting compounds using a parallel microfractionation-based bioassay. We successfully apply this method to screen VX, VM, and RVX nerve agents as well as methomyl, a carbamate pesticide, out of soil and whole blood samples at low μM to sub-μM concentrations. This methodology can be easily extended to diverse chemical families and biological activities of interest.

In-source fragmentation (ISF) is a naturally occurring phenomenon in various ion sources including soft ionization techniques such as matrix-assisted laser desorption/ionization (MALDI). It has traditionally been minimized as it makes the dataset more complex and often leads to mis-annotation of metabolites. Here, we introduce an approach termed PICA (for pixel intensity correlation analysis) that takes advantage of ISF in MALDI imaging to increase confidence in metabolite identification. In PICA, the extraction and association of in-source fragments to their precursor ion results in “pseudo-MS/MS spectra” that can be used for identification. We examined PICA using three different datasets, two of which were published previously and included validated metabolites annotation. We show that highly colocalized ions possessing Pearson correlation coefficient (PCC) ≥ 0.9 for a given precursor ion are mainly its in-source fragments, natural isotopes, adduct ions, or multimers. These ions provide rich information for their precursor ion identification. In addition, our results show that moderately colocalized ions (PCC < 0.9) may be structurally related to the precursor ion, which allows for the identification of unknown metabolites through known ones. Finally, we propose three strategies to reduce the total computation time for PICA in MALDI imaging. To conclude, PICA provides an efficient approach to extract and group ions stemming from the same metabolites in MALDI imaging and thus allows for high-confidence metabolite identification.

This paper presents a novel experimental approach to in-situ study of atmospheric phenomena such as nucleation scavenging by biological seeds, bio-droplet dehydration, and bioaerosol's particle scavenging by raindrops. Our methodology is based on the analysis of the dynamical changes of fluorescence signal. We use a remote sensing system based on a homebuilt hyperspectral laser induced fluorescence (LIF) Lidar to measure the transient back-fluorescence and backscattering signals. The spectral line shape of the transient fluorescence associated with an aerosolized tryptophan solution was first analyzed in the laboratory. It then used to study bioaerosol phase transitions between wet and dry conditions. The experiments were first conducted in a dynamic aerosol cell where we repetitively create and monitor the droplets containing bioaerosol cloud starting from its early formation till its total evaporation. The LIF-Lidar was used to simultaneously measure back-fluorescence, scattering and transmission. These measurements were synchronized with the generation of droplets containing bioaerosol and with the monitoring of aerosol's size distribution and ambient conditions. A novel optical receiver design was used to simultaneously detect both back-fluorescence polarization components. Results showed that along with droplet's evaporation process, bioaerosol's fluorescence spectrum exhibit a blue shift, known as the dynamic Stokes-shifts, of ∼2000 cm⁻¹ and an increase in its fluorescence anisotropy. To the best of our knowledge, this is the first report of fluorescence Stokes-shifts and anisotropy within microdroplets containing a biological solution due to wet-dry phase transitions. This method was also used to quantify scavenging of biological particle by raindrops from 100 m. It shows that valuable information can be derived from analyzing the fluorescence spectrum of bioaerosol within a cloud and demonstrate the potential of a LIF-LIDAR remote system to perform in-situ studies of scavenging processes.