Estimating the case fatality ratio for COVID-19 using a time-shifted distribution analysis.

Estimating the case fatality ratio (CFR) for COVID-19 is an important aspect of public health. However, calculating CFR accurately is problematic early in a novel disease outbreak, due to uncertainties regarding the time course of disease and difficulties in diagnosis and reporting of cases. In this work, we present a simple method for calculating the CFR using only public case and death data over time by exploiting the correspondence between the time distributions of cases and deaths. The time-shifted distribution (TSD) analysis generates two parameters of interest: the delay time between reporting of cases and deaths and the CFR. These parameters converge reliably over time once the exponential growth phase has finished. Analysis is performed for early COVID-19 outbreaks in many countries, and we discuss corrections to CFR values using excess-death and seroprevalence data to estimate the infection fatality ratio (IFR). While CFR values range from 0.2% to 20% in different countries, estimates for IFR are mostly around 0.5-0.8% for countries that experienced moderate outbreaks and 1-3% for severe outbreaks. The simplicity and transparency of TSD analysis enhance its usefulness in characterizing a new disease as well as the state of the health and reporting systems.

The role of the 2D-to-3D transition in x-ray diffraction analysis of crystallite size.

The diffraction behaviour of stacked layers of graphene and hexagonal boron nitride are studied computationally by direct calculation of the diffraction pattern using the Debye scattering equation. Analysis of the position and profile of the diffraction peaks show that while single-layer graphene is unambiguously a 2D material, ordered stacks of three or more layers diffract as bulk material. Following the Scherrer equation, we correlate the known crystallite size with the diffraction peak parameters and observe strong affine relationships which exist separately for single-layer, bi-layer and three or more layer (bulk) structures. We determine a series of expressions to calculate the crystallite size which do not suffer the well-known size-dependence or rely on assumptions about the shape. We present a detailed workflow showing how these expressions can be applied to experimental data.

Graphitization of Glassy Carbon after Compression at Room Temperature.

Glassy carbon is a technologically important material with isotropic properties that is nongraphitizing up to ∼3000 °C and displays complete or "superelastic" recovery from large compression. The pressure limit of these properties is not yet known. Here we use experiments and modeling to show permanent densification, and preferred orientation occurs in glassy carbon loaded to 45 GPa and above, where 45 GPa represents the limit to the superelastic and nongraphitizing properties of the material. The changes are explained by a transformation from its sp^{2} rich starting structure to a sp^{3} rich phase that reverts to fully sp^{2} bonded oriented graphite during pressure release.

Reaction paths of phosphine dissociation on silicon (001).

Using density functional theory and guided by extensive scanning tunneling microscopy (STM) image data, we formulate a detailed mechanism for the dissociation of phosphine (PH3) molecules on the Si(001) surface at room temperature. We distinguish between a main sequence of dissociation that involves PH2+H, PH+2H, and P+3H as observable intermediates, and a secondary sequence that gives rise to PH+H, P+2H, and isolated phosphorus adatoms. The latter sequence arises because PH2 fragments are surprisingly mobile on Si(001) and can diffuse away from the third hydrogen atom that makes up the PH3 stoichiometry. Our calculated activation energies describe the competition between diffusion and dissociation pathways and hence provide a comprehensive model for the numerous adsorbate species observed in STM experiments.

Reaction pathways for pyridine adsorption on silicon (0 0 1).

Density functional theory is used to describe the reactions of chemisorption of pyridine on the silicon (0 0 1) surface. Adsorption energies of six relevant structures, and the activation energies between them are reported. We consider in detail the dative to tight-bridge transition for which conflicting results have been reported in the literature, and provide a description of the formation of inter-row chains observed in high-coverage experiments. We demonstrate that the choice of DFT functional has a considerable effect on the relative energetics and of the four DFT functionals considered, we find that the range-separated hybrid ωB97X-D functional with empirical dispersion provides the most consistent description of the experiment data.

Density and structural effects in the radiation tolerance of TiO2 polymorphs.

The radiation response of TiO2 has been studied using molecular dynamics. The simulations are motivated by experimental observations that the three low-pressure polymorphs, rutile, brookite and anatase, exhibit vastly different tolerances to amorphization under ion-beam irradiation. To understand the role of structure we perform large numbers of simulations using the small thermal spike method. We quantify to high statistical accuracy the number of defects created as a function of temperature and structure type, and reproduce all the main trends observed experimentally. To evaluate a hypothesis that volumetric strain relative to the amorphous phase is an important driving force for defect recovery, we perform spike simulations in which the crystalline density is varied over a wide range. Remarkably, the large differences between the polymorphs disappear once the density difference is taken into account. This finding demonstrates that density is an important factor which controls radiation tolerance in TiO2.

Chemical evolution via beta decay: a case study in strontium-90.

Using (90)Sr as a representative isotope, we present a framework for understanding beta decay within the solid state. We quantify three key physical and chemical principles, namely momentum-induced recoil during the decay event, defect creation due to physical displacement, and chemical evolution over time. A fourth effect, that of electronic excitation, is also discussed, but this is difficult to quantify and is strongly material dependent. The analysis is presented for the specific cases of SrTiO(3) and SrH(2). By comparing the recoil energy with available threshold displacement data we show that in many beta-decay situations defects such as Frenkel pairs will not be created during decay as the energy transfer is too low. This observation leads to the concept of chemical evolution over time, which we quantify using density functional theory. Using a combination of Bader analysis, phonon calculations and cohesive energy calculations, we show that beta decay leads to counter-intuitive behavior that has implications for nuclear waste storage and novel materials design.

Nonequilibrium route to nanodiamond with astrophysical implications.

Nanometer-sized diamond grains are commonly found in primitive chondritic meteorites, but their origin is puzzling. Using evidence from atomistic simulation, we establish a mechanism by which nanodiamonds form abundantly in space in a two-stage process involving condensation of vapor to form carbon onions followed by transformation to nanodiamond in an energetic impact. This nonequilibrium process is consistent with common environments in space and invokes the fewest assumptions of any proposed model. Accordingly, our model can explain nanodiamond formation in both presolar and solar environments. The model provides an attractive framework for understanding noble gas incorporation and explains all key features of meteoritic nanodiamond, including size, shape, and polytype. By understanding the creation of nanodiamonds, new opportunities arise for their exploitation as a powerful astrophysical probe.

The origin of preferred orientation during carbon film growth.

Carbon films were prepared using a filtered cathodic vacuum arc deposition system operated with a substrate bias varying linearly with time during growth. Ion energies were in the range between 95 and 620 eV. Alternating dark, high density (sp(3) rich) bands and light, low density (sp(2) rich) bands were observed using cross-sectional transmission electron microscopy, corresponding to abrupt transitions between materials with densities of approximately 3.1 and 2.6 g cm(-3). No intermediate densities were observed in the samples. The low density bands show strong preferred orientation with graphitic sheets aligned normal to the film. After annealing, the low density bands became more oriented and the thinner high density layers were converted to low density material. In molecular dynamics modelling of film growth, temperature activated structural rearrangements occurring over long timescales ([Formula: see text] ps) caused the transition from sp(3) rich to oriented sp(2) rich structure. Once this oriented growth was initiated, the sputtering yield decreased and channelling was observed. However, we conclude that sputtering and channelling events, while they occur, are not the cause of the transition to the oriented structure.

Abrupt stress induced transformation in amorphous carbon films with a highly conductive transition phase.

We demonstrate that when, and only when, the biaxial stress is increased above a critical value of 6+/-1 GPa during the growth of a carbon film at room temperature, tetrahedral amorphous carbon is formed. This confirms that the stress present during the formation of an amorphous carbon film determines its sp;{3} bonding fraction. In the vicinity of the critical stress, a highly oriented graphitelike material is formed which exhibits low electrical resistance and provides Ohmic contacts to silicon. Atomistic simulations reveal that the structural transitions are thermodynamically driven and not the result of dynamical effects.

Dendritic cells from control but not atopic donors respond to contact and respiratory sensitizer treatment in vitro with differential cytokine production and altered stimulatory capacity.

BACKGROUND: Chemical haptens induce both contact and allergic respiratory disease with dendritic cells (DCs) controlling and directing immune responses in vivo. Contact and respiratory haptens may promote differential cytokine production yet distinguishing these effects in vitro remains difficult due to human donor variability. Objective We sought to determine the effect of atopic status on the ability of DC to respond to contact and respiratory sensitizer treatment in vitro as DC from atopic donors are believed to promote Th2-type responses. METHODS: Enriched DC from control or atopic donors were treated for 4 h with levels of the contact sensitizer 2,4-dinitrochlorobenzene (DNCB) or the respiratory sensitizer trimellitic anhydride (TMA) that did not reduce cell viability. A sensitive intracellular detection technique was used to measure cytokine production, while T cell responses were assessed in a mixed leucocyte reaction. RESULTS: DC from control, non-atopic, donors produced cytokines differentially in response to sensitizer treatment; DNCB treatment significantly increased the production of Th1 cytokines IL-12 and IFN-gamma while TMA induced the production of IL-13. Control donor DC treated with TMA stimulated less in a mixed leucocyte reaction than untreated cells with any response reduced further by blocking IL-13 in culture. However, DC from atopic donors showed no significant alteration in either cytokine production or T cell stimulatory capacity after sensitizer treatment. CONCLUSION: Haptens modulate DC by changing the production of cytokines that may play a role in T cell stimulation and subsequent polarization of the immune response. DC from atopic donors were unresponsive to chemical sensitizer treatment, and may be deficient in inducing divergent T cell responses.

Duplex-guided infrainguinal balloon angioplasty and stenting. A 4-year experience.

AIM: The traditional technique of infrainguinal arterial balloon angioplasties involves the use of fluoroscopy and contrast material. We performed these procedures under duplex guidance to eliminate radiation exposure and avoid nephrotoxic effect of contrast. METHODS: Over the last four years, 274 patients (59% males) with a mean age of 74+/-9 years (range 42-97 years) had a total of 360 attempted balloon angioplasties of the superficial femoral (SFA) and/or popliteal arteries under duplex guidance. Cannulation of common femoral artery, manipulation of the guidewire across the stenoses and/or occlusions of the SFA and/or popliteal artery, and balloon dilation were achieved with duplex guidance alone. Infrapopliteal angioplasties of 80 arteries were attempted in 54 cases (15% of all cases). RESULTS: Overall technical success for femoral-popliteal segment was 95% (342/360 cases) and 96% (77/80 cases) for infrapopliteal segment. CONCLUSION: Duplex guided balloon angioplasty and stent placement appears to be a safe and effective technique for treatment of femoral-popliteal and infrapopliteal arterial occlusive disease.

Single P and As dopants in the Si(001) surface.

Using first-principles density functional theory, we discuss doping of the Si(001) surface by a single substitutional phosphorus or arsenic atom. We show that there are two competing atomic structures for isolated Si-P and Si-As heterodimers, and that the donor electron is delocalized over the surface. We also show that the Si atom dangling bond of one of these heterodimer structures can be progressively charged by additional electrons. It is predicted that surface charge accumulation as a result of tip-induced band bending leads to structural and electronic changes of the Si-P and Si-As heterodimers which could be observed experimentally. Scanning tunneling microscopy (STM) measurements of the Si-P heterodimer on a n-type Si(001) surface reveal structural characteristics and a bias-voltage dependent appearance, consistent with these predictions. STM measurements for the As:Si(001) system are predicted to exhibit similar behavior to P:Si(001).

Inhaled allergen-driven CD1c up-regulation and enhanced antigen uptake by activated human respiratory-tract dendritic cells in atopic asthma.

BACKGROUND: Dendritic cells (DC) mediate inflammation in rodent models of allergic airway disease, but the role played by human respiratory-tract DC (hRTDC) in atopic asthma remains poorly defined. Recent data suggest that CD1 antigen presentation by hRTDC may contribute to asthma pathogenesis. OBJECTIVE: To investigate the influence of hRTDC on the balance between atopy and allergic asthma in human subjects and to determine whether CD1 expression by hRTDC is modulated during asthmatic inflammation. METHODS: Sputum cells were induced from steroid-naïve, allergen-challenged and allergen-naïve subjects (atopic asthmatics, atopic non-asthmatics and non-atopic controls). hRTDC were identified using monoclonal antibody labelling and analysis by flow cytometry. RESULTS: hRTDC stained HLA-DR(+) (negative for markers of other cell lineages) were predominantly myeloid and comprised approximately 0.5% of viable sputum cells. Sputum cells were potent stimulators of allogeneic CD4(+) naïve T cells and enrichment/depletion experiments correlated stimulatory potency with DC numbers. Sputum contained cells that exhibited typical dendritic morphology when analysed by electron microscopy. Myeloid hRTDC were endocytically active, but uptake of FITC-dextran was enhanced in cells from asthmatics (P<0.001). Despite their increased endocytic capacity, asthmatic myeloid hRTDC appeared mature and expressed increased levels of maturation markers (P<0.05-P<0.001), CD1c, CD1d and langerin (P<0.05). CD1c expression by asthmatic myeloid hRTDC was enhanced upon in vivo allergen challenge (three to ninefold within 24 h; P<0.05). CD11c(-)CD123(high) hRTDC were only detected in asthmatic sputum and were increased in number following allergen challenge. CONCLUSION: Despite limited cell numbers, it proved possible to analyse human RTDC in induced sputum, providing evidence that increased antigen uptake and enhanced CD1 presentation by activated hRTDC may contribute to allergic airway disease. CD1 presentation by hRTDC in atopic asthma may therefore constitute a novel target for future intervention strategies.

Duplex guided balloon angioplasty of failing infrainguinal bypass grafts.

OBJECTIVE: To assess the results of angioplasty and stent placement under duplex guidance for failing grafts. METHODS: Over 22 months, 25 patients (72% males) with a mean age of 74+/-10 years presented to our institution with a failing infrainguinal bypass. The site of the most significant stenotic lesion was in the inflow in four cases, conduit in 18 cases and at the outflow in 11 cases. All arterial (20) or graft (13) entry sites cannulations were performed under direct duplex visualization. Duplex scanning was the sole imaging modality used to manipulate the guide wire and directional catheters from the ipsilateral CFA to a site beyond the most distal stenotic lesion. Selection and placement of balloons and stents were also guided by duplex. In 11 cases (33%), the contralateral CFA was used as the entry site and a standard approach (fluoroscopy and contrast material) was employed. Completion duplex exams were obtained in all cases. RESULTS: The overall technical success was 97% (32/33 cases). In only one case, the outflow stenotic lesion in the plantar artery could not be traversed with the guidewire due to extreme tortuosity. Overall local complications rate was 6% (two cases). One vein bypass pseudoaneurysm caused by rupture with a cutting balloon was repaired by patch angioplasty and one SFA pseudoaneurysm at the puncture site required open repair. Overall 30-day survival rate was 100%. Overall 6-month limb salvage and primary patency rates were 100 and 69%, respectively. CONCLUSIONS: Duplex guided endovascular therapy is an effective modality for the treatment of failing infrainguinal arterial bypasses.

Phosphine dissociation on the Si(001) surface.

Density functional calculations are performed to identify features observed in STM experiments after phosphine (PH3) dosing of the Si(001) surface. On the basis of a comprehensive survey of possible structures, energetics, and simulated STM images, three prominent STM features are assigned to structures containing surface bound PH2, PH, and P, respectively. Collectively, the assigned features outline for the first time a detailed mechanism of PH3 dissociation and P incorporation on Si(001).