Among-site variability in the stochastic dynamics of East African coral reefs

Coral reefs are dynamic systems whose composition is highly influenced by unpredictable biotic and abiotic factors. Understanding the spatial scale at which long-term predictions of reef composition can be made will be crucial for guiding conservation efforts. Using a 22-year time series of benthic composition data from 20 reefs on the Kenyan and Tanzanian coast, we studied the long-term behaviour of Bayesian vector autoregressive state-space models for reef dynamics, incorporating among-site variability. We estimate that if there were no among-site variability, the total long-term variability would be approximately one third of its current value. Thus among-site variability contributes more to long-term variability in reef composition than does temporal variability. Individual sites are more predictable than previously thought, and predictions based on current snapshots are informative about long-term properties. Our approach allowed us to identify a subset of possible climate refugia sites with high conservation value, where the long-term probability of coral cover <= 0.1 was very low. Analytical results show that this probability is most strongly influenced by among-site variability and by interactions among benthic components within sites. These findings suggest that conservation initiatives might be successful at the site scale as well as the regional scale.Comment: 97 pages, 49 figure

Development of an N-1 perfusion process and optimized scale-down models for implementation in a platform CHO cell culture manufacturing process

The use of N-1 perfusion, coupled with high-inoculum fed batch in CHO cell culture manufacturing processes, has been shown to increase volumetric productivity and shorten the duration of the fed-batch production phase. Implementation of N-1 perfusion as part of a platform process requires the ability to screen multiple clones and to optimize media and process parameters in a high-throughput manner. We have developed an N-1 perfusion process, along with a series of scale-down models for N-1 perfusion using shake flasks, cell culture tubes, and deep-well plates. Process parameters for scale-down models were optimized to maximize comparability of growth profiles and cell culture performance relative to 5L N-1 perfusion bioreactors. Scale-down models were used to inoculate fed-batch experiments in Ambr15 micro-bioreactors at high seeding density, in order to compare growth and productivity profiles to those observed in 5L bench scale bioreactors. Multiple cell lines derived from different CHO hosts were evaluated in order to verify the robustness of the scale-down models. Results demonstrated that cell growth and viability in the optimized scale-down models were comparable to those observed in 5L N-1 perfusion bioreactors. Furthermore, growth, productivity, and product quality profiles from high-inoculum fed-batch experiments were comparable regardless of inoculum source. Optimized scale down models of N-1 perfusion, coupled with Ambr15 fed-batch production micro-bioreactors, have now been integrated into a high-throughput and robust workflow to enable DOE and screening experiments for clone selection, media development and parameter optimization in a platform N-1 perfusion process for monoclonal antibody manufacturing

Auggie: Encouraging Effortful Communication through Handcrafted Digital Experiences

Digital communication is often brisk and automated. From auto-completed messages to "likes," research has shown that such lightweight interactions can affect perceptions of authenticity and closeness. On the other hand, effort in relationships can forge emotional bonds by conveying a sense of caring and is essential in building and maintaining relationships. To explore effortful communication, we designed and evaluated Auggie, an iOS app that encourages partners to create digitally handcrafted Augmented Reality (AR) experiences for each other. Auggie is centered around crafting a 3D character with photos, animated movements, drawings, and audio for someone else. We conducted a two-week-long field study with 30 participants (15 pairs), who used Auggie with their partners remotely. Our qualitative findings show that Auggie participants engaged in meaningful effort through the handcrafting process, and felt closer to their partners, although the tool may not be appropriate in all situations. We discuss design implications and future directions for systems that encourage effortful communication.Comment: To appear at the 25th ACM Conference On Computer-Supported Cooperative Work And Social Computing (CSCW '22). 25 page

Report on the NSF Workshop on Formal Methods for Security

The NSF workshop on Security and Formal Methods, held 19--20 November 2015, brought together developers of formal methods, researchers exploring how to apply formal methods to various kinds of systems, and people familiar with the security problem space.Engineering and Applied Science

First principles study of toxic gas molecules adsorption on group IVA (C, Si, Ge) 2-dimensional materials

Two-dimensional materials from group IVA namely graphene, silicene, and germanene have gained research interest in various fields of applications recently due to their extraordinary properties. These substrates have been successfully synthesized and are found to have interesting gas sensing capabilities. In this work, first-principles study using density functional theory is carried out to investigate the adsorption of toxic gases such as CO, Cl2 , NO2 , and COCl2 on these monolayers. We analyze the best adsorption site and orientation for these molecules on the monolayers by calculating the adsorption energy. Charge transfer, the density of state (DOS) and band diagram calculations are performed to explore the changes in their electronic and structural properties due to the adsorbed gas molecules. As for the sensing performance, crude estimations of the sensitivity and recovery time are performed. The results show that silicene and germanene monolayers are better at detecting CO and NO2 as compared to graphene. They have a short recovery time for CO but a long recovery time for NO2 implying that they are better for scavenging NO2 . Besides, silicene is also a better gas sensor for chlorine gas with a 44 min recovery time. As for graphene, it is the best gas sensor for phosgene among the substrates. This study gives a clear prediction of substrates for the detection of these toxic gases

A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy

Infectious agents contribute significantly to the global burden of diseases through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 genome-wide association studies in 9,611 participants from UK Biobank, we identified NFKB1 as a locus associated with quantitative antibody responses to multiple pathogens, including those from the herpes, retro-, and polyoma-virus families. An insertion-deletion variant thought to affect NFKB1 expression (rs28362491), was mapped as the likely causal variant and could play a key role in regulation of the immune response. Using 121 infection- and inflammation-related traits in 487,297 UK Biobank participants, we show that the deletion allele was associated with an increased risk of infection from diverse pathogens but had a protective effect against allergic disease. We propose that altered expression of NFKB1, as a result of the deletion, modulates hematopoietic pathways and likely impacts cell survival, antibody production, and inflammation. Taken together, we show that disruptions to the tightly regulated immune processes may tip the balance between exacerbated immune responses and allergy, or increased risk of infection and impaired resolution of inflammation

Individual Oligodendrocytes Have Only a Few Hours in which to Generate New Myelin Sheaths In Vivo

The number of myelin sheaths made by individual oligodendrocytes regulates the extent of myelination, which profoundly affects central nervous system function. It remains unknown when, during their life, individual oligodendrocytes can regulate myelin sheath number in vivo. We show, using live imaging in zebrafish, that oligodendrocytes make new myelin sheaths during a period of just 5 hr, with regulation of sheath number after this time limited to occasional retractions. We also show that activation and reduction of Fyn kinase in oligodendrocytes increases and decreases sheath number per cell, respectively. Interestingly, these oligodendrocytes also generate their new myelin sheaths within the same period, despite having vastly different extents of myelination. Our data demonstrate a restricted time window relative to the lifetime of the individual oligodendrocyte, during which myelin sheath formation occurs and the number of sheaths is determined

Multiplexed genotyping of ABC transporter polymorphisms with the Bioplex suspension array

We have developed and validated a consolidated bead-based genotyping platform, the Bioplex suspension array for simultaneous detection of multiple single nucleotide polymorphisms (SNPs) of the ATP-binding cassette transporters. Genetic polymorphisms have been known to influence therapeutic response and risk of disease pathologies. Genetic screening for therapeutic and diagnostic applications thus holds great promise in clinical management. The allele-specific primer extension (ASPE) reaction was used to assay 22 multiplexed SNPs for eight subjects. Comparison of the microsphere-based ASPE assay results to sequencing results showed complete concordance in genotype assignments. The Bioplex suspension array thus proves to be a reliable, cost-effective and high-throughput technological platform for genotyping. It can be easily adapted to customized SNP panels for specific applications involving large-scale mutation screening of clinically relevant markers