Bostonia. Volume 3

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

Bostonia. Volume 11

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

Bayesian modeling of recombination events in bacterial populations

Background: We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases. Results: We introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker) implementing the model and the corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites. Conclusion: A multitude of challenging simulation scenarios and an analysis of real data from seven housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/ mnf//mate/jc/software/brat.html

Accurate Crystal Structure Prediction of New 2D Hybrid Organic Inorganic Perovskites

Low dimensional hybrid organic-inorganic perovskites (HOIPs) represent a promising class of electronically active materials for both light absorption and emission. The design space of HOIPs is extremely large, since a diverse space of organic cations can be combined with different inorganic frameworks. This immense design space allows for tunable electronic and mechanical properties, but also necessitates the development of new tools for in silico high throughput analysis of candidate structures. In this work, we present an accurate, efficient, transferable and widely applicable machine learning interatomic potential (MLIP) for predicting the structure of new 2D HOIPs. Using the MACE architecture, an MLIP is trained on 86 diverse experimentally reported HOIP structures. The model is tested on 73 unseen perovskite compositions, and achieves chemical accuracy with respect to the reference electronic structure method. Our model is then combined with a simple random structure search algorithm to predict the structure of hypothetical HOIPs given only the proposed composition. Success is demonstrated by correctly and reliably recovering the crystal structure of a set of experimentally known 2D perovskites. Such a random structure search is impossible with ab initio methods due to the associated computational cost, but is relatively inexpensive with the MACE potential. Finally, the procedure is used to predict the structure formed by a new organic cation with no previously known corresponding perovskite. Laboratory synthesis of the new hybrid perovskite confirms the accuracy of our prediction. This capability, applied at scale, enables efficient screening of thousands of combinations of organic cations and inorganic layers.Comment: 14 pages and 9 figures in the main text. Supplementary included in pd

Biomagnetic recovery of selenium: Bioaccumulating of selenium granules in magnetotactic bacteria

Using microorganisms to remove waste and/or neutralize pollutants from contaminated water is attracting much attention due to the environmentally friendly nature of this methodology. However, cell recovery remains a bottleneck and a considerable challenge for the development of this process. Magnetotactic bacteria are a unique group of organisms that can be manipulated by an external magnetic field due to the presence of biogenic magnetite crystals formed within their cells. In this study, we demonstrated the first account of accumulation and precipitation of amorphous elemental selenium nanoparticles within magnetotactic bacteria alongside and independently to magnetite crystal biomineralisation when grown in a medium containing selenium oxyanion (SeO3 (2-)). Quantitative analysis shows that magnetotactic bacteria accumulate the highest amount of target molecules (Se) per cell than any other previously reported of non-ferrous metal/metalloid. For example, 2.4 and 174 times more Se is accumulated when compared to Te uptaken into cells and Cd(2+) adsorption onto the cell surface respectively. Crucially, the bacteria with high levels of Se accumulation were successfully recovered with an external magnetic field. This biomagnetic recovery and effective accumulation of target elements demonstrate the potential for application in bioremediation of polluted water. IMPORTANCE: The development of a technique for effective environmental water remediation is urgently required across the globe. A biological remediation process of waste removal and/or neutralization of pollutant from contaminated water using microorganism has great potential, but cell recovery remains a bottleneck. Magnetotactic bacteria synthesize magnetic particles within their cells, which can be recovered by a magnetic field. Herein, we report the first example of accumulation and precipitation of amorphous elemental selenium nanoparticles within magnetotactic bacteria independent of magnetic particle synthesis. The cells were able to accumulate the highest amount of Se compared to other foreign elements. More importantly, the Se accumulating bacteria were successfully recovered with an external magnetic field. We believe magnetotactic bacteria confer unique advantages of biomagnetic cell recovery and of Se accumulation, providing a new and effective methodology for bioremediation of polluted water

The Vehicle, 1967, Vol. 9 no. 1

Vol. 9, No. 1 Table of Contents Commentarypage 3 PoofMolly J. Evanspage 4 PreludeMike Baldwinpage 5 UntitledMike Baldwinpage 5 Where is Tomorrow?Paula Bresnanpage 6 Could It Be Or NotMary Hoeggerpage 7 PsalmAnthony Griggspage 7 Where Am I Going?William A. Framepage 8 Out of DarknessMarilyn Henry Hoodpage 9 She CriedMolly J. Evanspage 12 When I MoveAnthony Griggspage 13 Hi Ya, MorningWilliam A. Framepage 13 Summer Twilight ThoughtsSteve Allenpage 14 Too MuchBill Moserpage 16 Ink SketchWilliam A. Framepage 17 No. 1Molly J. Evanspage 18 Youth, So Hated and DamnedJeff Hendrickspage 18 GoneJackie Jaquespage 19 The JesterWilliam A. Framepage 20 ReflectionMike Baldwinpage 20 No. 3Molly J. Evanspage 21 EpitaphBill Moserpage 22 I Take A Long-Out-of-Use BookAnthony Griggspage 23https://thekeep.eiu.edu/vehicle/1016/thumbnail.jp

The Vehicle, 1967, Vol. 9 no. 1

Vol. 9, No. 1 Table of Contents Commentarypage 3 PoofMolly J. Evanspage 4 PreludeMike Baldwinpage 5 UntitledMike Baldwinpage 5 Where is Tomorrow?Paula Bresnanpage 6 Could It Be Or NotMary Hoeggerpage 7 PsalmAnthony Griggspage 7 Where Am I Going?William A. Framepage 8 Out of DarknessMarilyn Henry Hoodpage 9 She CriedMolly J. Evanspage 12 When I MoveAnthony Griggspage 13 Hi Ya, MorningWilliam A. Framepage 13 Summer Twilight ThoughtsSteve Allenpage 14 Too MuchBill Moserpage 16 Ink SketchWilliam A. Framepage 17 No. 1Molly J. Evanspage 18 Youth, So Hated and DamnedJeff Hendrickspage 18 GoneJackie Jaquespage 19 The JesterWilliam A. Framepage 20 ReflectionMike Baldwinpage 20 No. 3Molly J. Evanspage 21 EpitaphBill Moserpage 22 I Take A Long-Out-of-Use BookAnthony Griggspage 23https://thekeep.eiu.edu/vehicle/1016/thumbnail.jp

Transplacental induction of membranous nephropathy in a neonate

We report a case of renal failure in a newborn infant due to membranous glomerulonephritis. The patient was anuric in the first 3 weeks of life, after which renal function recovered. The serum of the mother contained IgG antibodies which reacted with tubular brush borders and glomeruli of adult and fetal human kidneys. Reactivity with renal epithelium from human kidneys was detected. We suggest that a transplacental, passive Heymann nephritis-like mechanism was the pathogenesis of the neonate's symptoms, although the antigen(s) involved was shown not to be gp 330 or any of the renal antigens known to be involved in experimental nephropathies

Dynamic Local Structure in Caesium Lead Iodide: Spatial Correlation and Transient Domains

Metal halide perovskites are multifunctional semiconductors with tunable structures and properties. They are highly dynamic crystals with complex octahedral tilting patterns and strongly anharmonic atomic behavior. In the higher temperature, higher symmetry phases of these materials, several complex structural features are observed. The local structure can differ greatly from the average structure and there is evidence that dynamic 2D structures of correlated octahedral motion form. An understanding of the underlying complex atomistic dynamics is, however, still lacking. In this work, the local structure of the inorganic perovskite CsPbI3 is investigated using a new machine learning force field based on the atomic cluster expansion framework. Through analysis of the temporal and spatial correlation observed during large-scale simulations, it is revealed that the low frequency motion of octahedral tilts implies a double-well effective potential landscape, even well into the cubic phase. Moreover, dynamic local regions of lower symmetry are present within both higher symmetry phases. These regions are planar and the length and timescales of the motion are reported. Finally, the spatial arrangement of these features and their interactions are investigated and visualized, providing a comprehensive picture of local structure in the higher symmetry phases