Most mathematical models for the spread of disease use differential equations based on uniform mixing assumptions or ad hoc models for the contact process. Here we explore the use of dynamic bipartite graphs to model the physical contact patterns that result from movements of individuals between specific locations. The graphs are generated by large-scale individual-based urban traffic simulations built on actual census, land-use and population-mobility data. We find that the contact network among people is a strongly connected small-world-like graph with a well-defined scale for the degree distribution. However, the locations graph is scale-free, which allows highly efficient outbreak detection by placing sensors in the hubs of the locations network. Within this large-scale simulation framework, we then analyse the relative merits of several proposed mitigation strategies for smallpox spread. Our results suggest that outbreaks can be contained by a strategy of targeted vaccination combined with early detection without resorting to mass vaccination of a population.

As an essential component of innate immunity, macrophages have multiple functions in both inhibiting or promoting cell proliferation and tissue repair. Diversity and plasticity are hallmarks of macrophages. Classical M1 and alternative M2 activation of macrophages, mirroring the Th1–Th2 polarization of T cells, represent two extremes of a dynamic changing state of macrophage activation. M1-type macrophages release cytokines that inhibit the proliferation of surrounding cells and damage contiguous tissue, and M2-type macrophages release cytokines that promote the proliferation of contiguous cells and tissue repair. M1–M2 polarization of macrophage is a tightly controlled process entailing a set of signaling pathways, transcriptional and posttranscriptional regulatory networks. An imbalance of macrophage M1–M2 polarization is often associated with various diseases or inflammatory conditions. Therefore, identification of the molecules associated with the dynamic changes of macrophage polarization and understanding their interactions is crucial for elucidating the molecular basis of disease progression and designing novel macrophage-mediated therapeutic strategies.

Background Coronavirus disease 2019 (COVID-19) has become a public health emergency. The widely used reverse transcription–polymerase chain reaction (RT-PCR) method has limitations for clinical diagnosis and treatment. Methods A total of 323 samples from 76 COVID-19–confirmed patients were analyzed by droplet digital PCR (ddPCR) and RT-PCR based 2 target genes (ORF1ab and N). Nasal swabs, throat swabs, sputum, blood, and urine were collected. Clinical and imaging data were obtained for clinical staging. Results In 95 samples that tested positive by both methods, the cycle threshold (Ct) of RT-PCR was highly correlated with the copy number of ddPCR (ORF1ab gene, R2 = 0.83; N gene, R2 = 0.87). Four (4/161) negative and 41 (41/67) single-gene positive samples tested by RT-PCR were positive according to ddPCR with viral loads ranging from 11.1 to 123.2 copies/test. The viral load of respiratory samples was then compared and the average viral load in sputum (17 429 ± 6920 copies/test) was found to be significantly higher than in throat swabs (2552 ± 1965 copies/test, P < .001) and nasal swabs (651 ± 501 copies/test, P < .001). Furthermore, the viral loads in the early and progressive stages were significantly higher than that in the recovery stage (46 800 ± 17 272 vs 1252 ± 1027, P < .001) analyzed by sputum samples. Conclusions Quantitative monitoring of viral load in lower respiratory tract samples helps to evaluate disease progression, especially in cases of low viral load.

To gain insight into how mutant huntingtin (mHtt) CAG repeat length modifies Huntington’s disease (HD) pathogenesis, we profiled mRNA in over 600 brain and peripheral tissue samples from HD knock-in mice with increasing CAG repeat lengths. We find repeat length dependent transcriptional signatures are prominent in the striatum, less so in cortex, and minimal in the liver. Co-expression network analyses reveal 13 striatal and 5 cortical modules that are highly correlated with CAG length and age, and that are preserved in HD models and some in the patients. Top striatal modules implicate mHtt CAG length and age in graded impairment of striatal medium spiny neuron identity gene expression and in dysregulation of cAMP signaling, cell death, and protocadherin genes. Importantly, we used proteomics to confirm 790 genes and 5 striatal modules with CAG length-dependent dysregulation at both RNA and protein levels, and validated 22 striatal module genes as modifiers of mHtt toxicities in vivo.

Severe acute respiratory syndrome coronavirus (SARS-CoV

Thermally removable nanoparticle templates were used for the fabrication of self-supported N-doped mesoporous carbons with a trace amount of Fe (Fe-N/C). Experimentally Fe-N/C was prepared by pyrolysis of poly(2-fluoroaniline) (P2FANI) containing a number of FeO(OH) nanorods that were prepared by a one-pot hydrothermal synthesis and homogeneously distributed within the polymer matrix. The FeO(OH) nanocrystals acted as rigid templates to prevent the collapse of P2FANI during the carbonization process, where a mesoporous skeleton was formed with a medium surface area of about 400 m(2)/g. Subsequent thermal treatments at elevated temperatures led to the decomposition and evaporation of the FeO(OH) nanocrystals and the formation of mesoporous carbons with the surface area markedly enhanced to 934.8 m(2)/g. Electrochemical measurements revealed that the resulting mesoporous carbons exhibited apparent electrocatalytic activity for oxygen reduction reactions (ORR), and the one prepared at 800 °C (Fe-N/C-800) was the best among the series, with a more positive onset potential (+0.98 V vs RHE), higher diffusion-limited current, higher selectivity (number of electron transfer n > 3.95 at +0.75 V vs RHE), much higher stability, and stronger tolerance against methanol crossover than commercial Pt/C catalysts in a 0.1 M KOH solution. The remarkable ORR performance was attributed to the high surface area and sufficient exposure of electrocatalytically active sites that arose primarily from N-doped carbons with minor contributions from Fe-containing species.

Upland cotton is the most important natural-fiber crop. The genomic variation of diverse germplasms and alleles underpinning fiber quality and yield should be extensively explored. Here, we resequenced a core collection comprising 419 accessions with 6.55-fold coverage depth and identified approximately 3.66 million SNPs for evaluating the genomic variation. We performed phenotyping across 12 environments and conducted genome-wide association study of 13 fiber-related traits. 7,383 unique SNPs were significantly associated with these traits and were located within or near 4,820 genes; more associated loci were detected for fiber quality than fiber yield, and more fiber genes were detected in the D than the A subgenome. Several previously undescribed causal genes for days to flowering, fiber length, and fiber strength were identified. Phenotypic selection for these traits increased the frequency of elite alleles during domestication and breeding. These results provide targets for molecular selection and genetic manipulation in cotton improvement.

Substitutional doping of transition metal dichalcogenides (TMDs) may provide routes to achieving tunable p-n junctions, bandgaps, chemical sensitivity, and magnetism in these materials. In this study, we demonstrate in situ doping of monolayer molybdenum disulfide (MoS2) with manganese (Mn) via vapor phase deposition techniques. Successful incorporation of Mn in MoS2 leads to modifications of the band structure as evidenced by photoluminescence and X-ray photoelectron spectroscopy, but this is heavily dependent on the choice of substrate. We show that inert substrates (i.e., graphene) permit the incorporation of several percent Mn in MoS2, while substrates with reactive surface terminations (i.e., SiO2 and sapphire) preclude Mn incorporation and merely lead to defective MoS2. The results presented here demonstrate that tailoring the substrate surface could be the most significant factor in substitutional doping of TMDs with non-TMD elements.