Improving food production from livestock

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Random Geometric Graphs

We analyse graphs in which each vertex is assigned random coordinates in a geometric space of arbitrary dimensionality and only edges between adjacent points are present. The critical connectivity is found numerically by examining the size of the largest cluster. We derive an analytical expression for the cluster coefficient which shows that the graphs are distinctly different from standard random graphs, even for infinite dimensionality. Insights relevant for graph bi-partitioning are included.Comment: 16 pages, 10 figures. Minor changes. Added reference

Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense

cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes are signaling proteins that initiate antiviral immunity in animal cells and cyclic-oligonucleotide-based anti-phage signaling system (CBASS) phage defense in bacteria. Upon phage recognition, bacterial CD-NTases catalyze synthesis of cyclic-oligonucleotide signals, which activate downstream effectors and execute cell death. How CD-NTases control nucleotide selection to specifically induce defense remains poorly defined. Here, we combine structural and nucleotide-analog interference-mapping approaches to identify molecular rules controlling CD-NTase specificity. Structures of the cyclic trinucleotide synthase Enterobacter cloacae CdnD reveal coordinating nucleotide interactions and a possible role for inverted nucleobase positioning during product synthesis. We demonstrate that correct nucleotide selection in the CD-NTase donor pocket results in the formation of a thermostable-protein-nucleotide complex, and we extend our analysis to establish specific patterns governing selectivity for each of the major bacterial CD-NTase clades A&ndash;H. Our results explain CD-NTase specificity and enable predictions of nucleotide second-messenger signals within diverse antiviral systems. &nbsp;</p

Bostonia: The Boston University Alumni Magazine. Volume 9

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

Direct experimental evidence for substrate adatom incorporation into a molecular overlayer

While the phenomenon of metal substrate adatom incorporation into molecular overlayers is generally believed to occur in several systems, the experimental evidence for this relies on the interpretation of scanning tunnelling microscopy (STM) images, which can be ambiguous and provides no quantitative structural information. We show that surface X- ray diffraction (SXRD) uniquely provides unambiguous identification of these metal adatoms. We present the results of a detailed structural study of the Au(111)-F4TCNQ system, combining surface characterisation by STM, low energy electron diffraction and soft X-ray photoelectron spectroscopy with quantitative experimental structural information from normal incidence X-ray standing waves (NIXSW) and SXRD, together with dispersion corrected density functional theory (DFT) calculations. Excellent agreement is found between the NIXSW data and the DFT calculations regarding the height and conformation of the adsorbed molecule, which has a twisted geometry rather than the previously supposed inverted bowl shape. SXRD measurements provide unequivocal evidence for the presence and location of Au adatoms, while the DFT calculations show this reconstruction to be strongly energetically favoured.Comment: 38 pages, 10 figure

Direct experimental evidence for substrate adatom incorporation into a molecular overlayer

While the phenomenon of metal substrate adatom incorporation into molecular overlayers is generally believed to occur in several systems, the experimental evidence for this relies on the interpretation of scanning tunneling microscopy (STM) images, which can be ambiguous and provides no quantitative structural information. We show that surface X-ray diffraction (SXRD) uniquely provides unambiguous identification of these metal adatoms. We present the results of a detailed structural study of the Au(111)-F4TCNQ system, combining surface characterization by STM, low-energy electron diffraction, and soft X-ray photoelectron spectroscopy with quantitative experimental structural information from normal incidence X-ray standing wave (NIXSW) and SXRD, together with dispersion-corrected density functional theory (DFT) calculations. Excellent agreement is found between the NIXSW data and the DFT calculations regarding the height and conformation of the adsorbed molecule, which has a twisted geometry rather than the previously supposed inverted bowl shape. SXRD measurements provide unequivocal evidence for the presence and location of Au adatoms, while the DFT calculations show this reconstruction to be strongly energetically favored

Direct experimental evidence for substrate adatom incorporation into a molecular overlayer

While the phenomenon of metal substrate adatom incorporation into molecular overlayers is generally believed to occur in several systems, the experimental evidence for this relies on the interpretation of scanning tunneling microscopy (STM) images, which can be ambiguous and provides no quantitative structural information. We show that surface X-ray diffraction (SXRD) uniquely provides unambiguous identification of these metal adatoms. We present the results of a detailed structural study of the Au(111)-F4TCNQ system, combining surface characterization by STM, low-energy electron diffraction, and soft X-ray photoelectron spectroscopy with quantitative experimental structural information from normal incidence X-ray standing wave (NIXSW) and SXRD, together with dispersion-corrected density functional theory (DFT) calculations. Excellent agreement is found between the NIXSW data and the DFT calculations regarding the height and conformation of the adsorbed molecule, which has a twisted geometry rather than the previously supposed inverted bowl shape. SXRD measurements provide unequivocal evidence for the presence and location of Au adatoms, while the DFT calculations show this reconstruction to be strongly energetically favored

A Combined Subaru/VLT/MMT 1--5 Micron Study of Planets Orbiting HR 8799: Implications for Atmospheric Properties, Masses, and Formation

We present new 1--1.25 micron (z and J band) Subaru/IRCS and 2 micron (K band) VLT/NaCo data for HR 8799 and a rereduction of the 3--5 micron MMT/Clio data first presented by Hinz et al. (2010). Our VLT/NaCo data yields a detection of a fourth planet at a projected separation of ~ 15 AU -- "HR 8799e". We also report new, albeit weak detections of HR 8799b at 1.03 microns and 3.3 microns. Empirical comparisons to field brown dwarfs show that at least HR 8799b and HR8799c, and possibly HR 8799d, have near-to-mid IR colors/magnitudes significantly discrepant from the L/T dwarf sequence. Standard cloud deck atmosphere models appropriate for brown dwarfs provide only (marginally) statistically meaningful fits to HR 8799b and c for unphysically small radii. Models with thicker cloud layers not present in brown dwarfs reproduce the planets' SEDs far more accurately and without the need for rescaling the planets' radii. Our preliminary modeling suggests that HR 8799b has log(g) = 4--4.5, Teff = 900K, while HR 8799c, d, and (by inference) e have log(g) = 4--4.5, Teff = 1000--1200K. Combining results from planet evolution models and new dynamical stability limits implies that the masses of HR 8799b, c, d, and e are 6--7 Mj, 7--10 Mj, 7--10 Mj and 7--10 Mj. 'Patchy" cloud prescriptions may provide even better fits to the data and may lower the estimated surface gravities and masses. Finally, contrary to some recent claims, forming the HR 8799 planets by core accretion is still plausible, although such systems are likely rare.Comment: 27 pages, 15 figures, Accepted for publication in The Astrophysical Journa

Opportunistic experiments to constrain aerosol effective radiative forcing

Aerosol–cloud interactions (ACIs) are considered to be the most uncertain driver of present-day radiative forcing due to human activities. The nonlinearity of cloud-state changes to aerosol perturbations make it challenging to attribute causality in observed relationships of aerosol radiative forcing. Using correlations to infer causality can be challenging when meteorological variability also drives both aerosol and cloud changes independently. Natural and anthropogenic aerosol perturbations from well-defined sources provide “opportunistic experiments” (also known as natural experiments) to investigate ACI in cases where causality may be more confidently inferred. These perturbations cover a wide range of locations and spatiotemporal scales, including point sources such as volcanic eruptions or industrial sources, plumes from biomass burning or forest fires, and tracks from individual ships or shipping corridors. We review the different experimental conditions and conduct a synthesis of the available satellite datasets and field campaigns to place these opportunistic experiments on a common footing, facilitating new insights and a clearer understanding of key uncertainties in aerosol radiative forcing. Cloud albedo perturbations are strongly sensitive to background meteorological conditions. Strong liquid water path increases due to aerosol perturbations are largely ruled out by averaging across experiments. Opportunistic experiments have significantly improved process-level understanding of ACI, but it remains unclear how reliably the relationships found can be scaled to the global level, thus demonstrating a need for deeper investigation in order to improve assessments of aerosol radiative forcing and climate change