Wright-Fisher diffusion bridges

The trajectory of the frequency of an allele which begins at $x$ at time $0$ and is known to have frequency $z$ at time $T$ can be modelled by the bridge process of the Wright-Fisher diffusion. Bridges when $x=z=0$ are particularly interesting because they model the trajectory of the frequency of an allele which appears at a time, then is lost by random drift or mutation after a time $T$. The coalescent genealogy back in time of a population in a neutral Wright-Fisher diffusion process is well understood. In this paper we obtain a new interpretation of the coalescent genealogy of the population in a bridge from a time $t\in (0,T)$. In a bridge with allele frequencies of 0 at times 0 and $T$ the coalescence structure is that the population coalesces in two directions from $t$ to $0$ and $t$ to $T$ such that there is just one lineage of the allele under consideration at times $0$ and $T$. The genealogy in Wright-Fisher diffusion bridges with selection is more complex than in the neutral model, but still with the property of the population branching and coalescing in two directions from time $t\in (0,T)$. The density of the frequency of an allele at time $t$ is expressed in a way that shows coalescence in the two directions. A new algorithm for exact simulation of a neutral Wright-Fisher bridge is derived. This follows from knowing the density of the frequency in a bridge and exact simulation from the Wright-Fisher diffusion. The genealogy of the neutral Wright-Fisher bridge is also modelled by branching P\'olya urns, extending a representation in a Wright-Fisher diffusion. This is a new very interesting representation that relates Wright-Fisher bridges to classical urn models in a Bayesian setting. This paper is dedicated to the memory of Paul Joyce

Highly Selective Hydrogenation of Furfural to Cyclopentanone over a NiFe Bimetallic Catalyst in a Methanol/Water Solution with a Solvent Effect

The aqueous phase hydrogenation of furfural to cyclopentanone over a NiFe bimetallic catalyst was investigated for the efficient utilization of biomass-derived compounds. Catalyst characterization by XRD, EDS mapping, and TPR revealed significant synergetic effects in the NiFe/SBA-15 catalyst. With NiFe/SBA-15, cyclopentanone selectivity was increased to 78.4% from 46.1% with Ni/SBA-15. The use of different supports showed that weak acidity favors cyclopentanone formation. The solvent played an important role: methanol/water solutions with different compositional ratios gave significantly changed product distributions. With pure methanol, and methanol-dominated and water-dominated solutions, respectively, the main product was furfuryl alcohol, tetrahydrofurfuryl alcohol, and cyclopentanone. Furfural in the water inhibited THFA formation, which led furfural to preferentially produce cyclopentanone. At the optimized reaction temperature, NiFe/SBA-15 in water gave 99.8% furfural conversion and 90% cyclopentanone yield at 300 min, which was much better than most reported nonprecious metal catalysts

Supported Ultrafine NiCo Bimetallic Alloy Nanoparticles Derived from Bimetal–Organic Frameworks: A Highly Active Catalyst for Furfuryl Alcohol Hydrogenation

Highly dispersed NiCo bimetallic alloy nanoparticles have been successfully immobilized on the SiO₂ frameworks by using heteronuclear metal–organic frameworks (MOFs) as metal alloy precursors. Catalyst characterizations revealed that the average size of NiCo alloy particles was less than 1 nm, with a total metal loading of about 20 wt %. As compared to individual Ni or Co MOF-derived catalysts and the catalysts prepared by the conventional impregnation method, the ultrafine NiCo/SiO₂-MOF catalyst showed a much better catalytic performance in the catalytic hydrogenation of furfuryl alcohol (FA) to tetrahydrofurfuryl alcohol (THFA) under mild conditions, giving 99.8% conversion of FA and 99.1% selectivity to THFA. It was found that a significant synergistic effect existed between Co and Ni within the subnanometer NiCo/SiO₂-MOF catalyst, which was 2 and 20 times more active than Ni/SiO₂-MOF and Co/SiO₂-MOF, respectively

Image_1_Comparison of dynamic visual acuity after implantation of toric bifocal or trifocal intraocular lens in age-related cataract patients: a randomized controlled trial.TIF

PurposeTo investigate the dynamic visual acuity (DVA) after implantation of toric bifocal or trifocal intraocular lens in age-related cataract patients.MethodsThis was a prospective randomized controlled trial. Of one hundred and twenty-four patients enrolled and randomized to receive unilateral phacoemulsification and toric trifocal (939 M/MP, Carl Zeiss Meditec AG, Jena, Germany) or toric bifocal (909 M, Carl Zeiss Meditec AG, Jena, Germany) intraocular lenses (IOL) implantation, ninety-nine patients completed the follow-up and were included in final analysis. Postoperatively, uncorrected and corrected distance (UDVA and CDVA), intermediate (UIVA and DCIVA) and near (UNVA and DCNVA) static visual acuity, manifest refraction and uncorrected and corrected distance DVA (UDDVA and CDDVA) at 20, 40 and 80 degrees per second (dps) were evaluated at one week, one month and three months.ResultsThree months postoperatively, the UDVA were 0.13 ± 0.11 and 0.14 ± 0.13 in the toric trifocal and bifocal IOL group, respectively. Significant better UIVA (trifocal, 0.17 ± 0.13 vs. bifocal, 0.23 ± 0.13, p = 0.037) and DCIVA (trifocal, 0.16 ± 0.11 vs. bifocal, 0.20 ± 0.12, p = 0.048) were observed in patients implanting toric trifocal than bifocal IOL at three months postoperatively. Patients implanted with toric bifocal IOL obtained better CDDVA at 80 dps (0.5607 ± 0.2032) than the trifocal group (0.6573 ± 0.2450, p = 0.039) at three months. Postoperative UDDVA and CDDVA at 20, 40 and 80 dps were significantly associated with age (p ConclusionToric trifocal IOL provides better static intermediate visual acuity, and toric bifocal IOL implantation provides better distance dynamic visual acuity at high speed.</p

Preparation and Characterization of Maillard Reaction Products from a Trinary System Composed of the Soy Protein Isolate, Chitosan Oligosaccharide, and Gum Arabic

To extend the application of chitosan oligosaccharide (COS) in complex coacervation between the soy protein isolate (SPI) and gum Arabic (GA), Maillard reaction among SPI, COS, and GA was induced under different conditions. High-performance gel permeation chromatography and sodium dodecyl sulfate polyacrylamide gel electrophoresis illustrated that products with high molecular weights (1.17 × 106 and 2.79 × 106 Da) were generated in the trinary system, and the Maillard reaction promoted the cross-linking of SPI, COS, and GA. The Maillard reaction was observed the most under conditions where SPI, COS, and GA (4:2:4, w/w) were kept at 80 °C for 12 h, and the results of thermogravimetry indicated that Maillard reaction products (MRPs) with the best thermal stability, which were positively charged, were generated. The results revealed that the extent of Maillard reaction was enhanced with the increase of time SPI being involved in the complex rather than GA. X-ray diffraction and Fourier transform infrared analysis indicated that Maillard reactions between SPI, COS, and GA under different conditions did not impact the crystal particle structures among them. Even though the extent of Maillard reaction among SPI, COS, and GA was lower than that between SPI and COS, MRPs with various viscoelastic properties were obtained under different conditions. Thus, as one kind of difunctional reactant in Maillard reaction, COS could react with either proteins or polysaccharides, and the MRPs have potential utilization in the food industry

Improving the GeAsSe Ovonic Threshold Switching Characteristics by Carbon Buffer Layers for Ultralow Leakage Current (∼0.4 nA) and Low Drift Characteristics

Volatile Ovonic threshold switching (OTS) selectors have been regarded as the critical component of highly integrated three-dimensional (3D) cross-point array nonvolatile memory systems. However, relatively high leakage current hinders the further reduction of power consumption in the crossbar array. In addition, the threshold voltage drift phenomenon hinders the improvement of device reliability. Utilizing the buffer layer can effectively reduce the interaction between electrodes and the active layer in the cross-point architecture. Here, it manifests that leakage current can be reduced to ∼0.4 nA with a 5 nm thick amorphous carbon layer as a buffer layer in the GeAsSe-based OTS device, where the carbon layer stabilizes the composition of GeAsSe during the electrical switching cycles. It is also found that the carbon layer leads to a lower threshold voltage drift (35.6 mv/dec) and excellent endurance (>109 cycles with ∼0.4 nA ON-state current). The conduction mechanism analysis demonstrates that the inhibition of the carbon layer on drift originates from the high barrier height from delocalized states transformed into localized states. This work clearly demonstrates the role of the carbon layer and facilitates future 3D crossbar-storage technology applications

Poly(methyl methacrylate)-Based Nanofluidic Device for Rapid and Multiplexed Serological Antibody Detection of SARS-CoV‑2

The outbreak of SARS-CoV-2 has emphasized the value of point-of-care diagnostics, as well as reliable and cost-effective serological antibody tests, to monitor the viral spread and contain pandemics and endemics. Here, we present a three-dimensional (3D) nanofluidic device for rapid and multiplexed detection of viral antibodies. The device is made from poly­(methyl methacrylate) and contains 3D fluidic channels with nanoscale topography variations on the millimeter length scale, enabled by combining gray-scale e-beam lithography and nanoimprint lithography. It works with capillary pumps only and does not require a complex microfluidic setup and pumps, which hinder the widespread usage of micro- and nanofluidic devices. The device is designed to size dependently immobilize particles from a multiparticle mixture at predefined positions in nanochannels, resulting in distinct trapping lines. We show that it can be used as an on-chip fluorescence-linked immunosorbent assay for highly specific and sensitive multiplexed detection of serological antibodies against different viral proteins. Further test flexibility is demonstrated by on-bead color multiplexing for simultaneous detection of IgG and IgM antibodies in convalescent human serum. The particle sorting is further leveraged to enable concurrent detection of anti-spike (SARS-CoV-2) and anti-hemagglutinin (influenza A) antibodies. The device’s applications can be further extended to detect a large variety of diseases simultaneously in a reliable and straightforward manner

Poly(methyl methacrylate)-Based Nanofluidic Device for Rapid and Multiplexed Serological Antibody Detection of SARS-CoV‑2

The outbreak of SARS-CoV-2 has emphasized the value of point-of-care diagnostics, as well as reliable and cost-effective serological antibody tests, to monitor the viral spread and contain pandemics and endemics. Here, we present a three-dimensional (3D) nanofluidic device for rapid and multiplexed detection of viral antibodies. The device is made from poly­(methyl methacrylate) and contains 3D fluidic channels with nanoscale topography variations on the millimeter length scale, enabled by combining gray-scale e-beam lithography and nanoimprint lithography. It works with capillary pumps only and does not require a complex microfluidic setup and pumps, which hinder the widespread usage of micro- and nanofluidic devices. The device is designed to size dependently immobilize particles from a multiparticle mixture at predefined positions in nanochannels, resulting in distinct trapping lines. We show that it can be used as an on-chip fluorescence-linked immunosorbent assay for highly specific and sensitive multiplexed detection of serological antibodies against different viral proteins. Further test flexibility is demonstrated by on-bead color multiplexing for simultaneous detection of IgG and IgM antibodies in convalescent human serum. The particle sorting is further leveraged to enable concurrent detection of anti-spike (SARS-CoV-2) and anti-hemagglutinin (influenza A) antibodies. The device’s applications can be further extended to detect a large variety of diseases simultaneously in a reliable and straightforward manner

Data_Sheet_1_Transcriptomic and metabolomic analysis reveals the influence of carbohydrates on lignin degradation mediated by Bacillus amyloliquefaciens.zip

IntroductionLigninolytic bacteria can secrete extracellular enzymes to depolymerize lignin into small-molecular aromatics that are subsequently metabolized and funneled into the TCA cycle. Carbohydrates, which are the preferred carbon sources of bacteria, influence the metabolism of lignin-derived aromatics through bacteria.MethodsIn this study, untargeted metabolomics and transcriptomics analyses were performed to investigate the effect of carbohydrates on lignin degradation mediated by Bacillus amyloliquefaciens MN-13, a strain with lignin-degrading activity that was isolated in our previous work.ResultsThe results demonstrated that the cell growth of the MN-13 strain and lignin removal were promoted when carbohydrates such as glucose and sodium carboxymethyl cellulose were added to an alkaline lignin-minimal salt medium (AL-MSM) culture. Metabolomics analysis showed that lignin depolymerization took place outside the cells, and the addition of glucose regulated the uptake and metabolism of lignin-derived monomers and activated the downstream metabolism process in cells. In the transcriptomics analysis, 299 DEGs were screened after 24 h of inoculation in AL-MSM with free glucose and 2 g/L glucose, respectively, accounting for 8.3% of the total amount of annotated genes. These DEGs were primarily assigned to 30 subcategories, including flagellar assembly, the PTS system, RNA degradation, glycolysis/gluconeogenesis, the TCA cycle, pyruvate metabolism, and tryptophan metabolism. These subcategories were closely associated with the cell structure, generation of cellular energy, and precursors for biosynthetic pathways, based on a − log 10 (P adjust) value in the KEGG pathway analysis.ConclusionIn summary, the addition of glucose increased lignin degradation mediated by the MN-13 strain through regulating glycolysis, TCA cycle, and central carbon metabolism.</p