Scalable Syriac Paleography using Interactive Visualization

Syriac (a dialect of Aramaic) was the primary language spoken in the late ancient Middle East between the second and eighth centuries AD, and continues to be a language of Christian scholarship and liturgy up to the present day. There are approximately 20,000 known surviving Syriac manuscripts. Among early manuscripts, only around 10% include a scribal note that provides information regarding when, where, and by whom a given manuscript was written. For the remaining 90%, close examination of subtle differences in the handwritten script remains the primary tool for determining provenance. Prior to this study, scholars classified early Syriac manuscripts into two divergent script styles: Estrangela and Serto. In this paper, we present a case study of historians’ analysis of this collection of manuscripts supported by visual analytic tools. This approach uncovered major inaccuracies in this dichotomous model, resulting in profound disruption to the dominant understanding of the development of these texts

Soil Modification by Invasive Plants: Effects on Native and Invasive Species of Mixed-Grass Prairies

Invasive plants are capable of modifying attributes of soil to facilitate further invasion by conspecifics and other invasive species. We assessed this capability in three important plant invaders of grasslands in the Great Plains region of North America: leafy spurge (Euphorbia esula), smooth brome (Bromus inermis) and crested wheatgrass (Agropyron cristatum). In a glasshouse, these three invasives or a group of native species were grown separately through three cycles of growth and soil conditioning in both steam-pasteurized and non-pasteurized soils, after which we assessed seedling growth in these soils. Two of the three invasive species, Bromus and Agropyron, exhibited significant self-facilitation via soil modification. Bromus and Agropyron also had significant facilitative effects on other invasives via soil modification, while Euphorbia had significant antagonistic effects on the other invasives. Both Agropyron and Euphorbia consistently suppressed growth of two of three native forbs, while three native grasses were generally less affected. Almost all intra- and interspecific effects of invasive soil conditioning were dependent upon presence of soil biota from field sites where these species were successful invaders. Overall, these results suggest that that invasive modification of soil microbiota can facilitate plant invasion directly or via ‘cross-facilitation’ of other invasive species, and moreover has potential to impede restoration of native communities after removal of an invasive species. However, certain native species that are relatively insensitive to altered soil biota (as we observed in the case of the forb Linum lewisii and the native grasses), may be valuable as ‘nurse’ species in restoration efforts

Challenging the Estrangela / Serto Divide: Why the Standard Model of Syriac Scripts Just Doesn\u27t Work

As part of a larger digital paleography project, our team has assembled a database of tens of thousands of individual Syriac letters and letter data from 96% of extant early Syriac manuscripts that have a secure composition date. Long term, such data can help scholars develop more accurate ways to classify Syriac scripts. In the present article we use this data to illustrate just how frequently the most common way of categorizing Syriac scripts as either Estrangela or Serto does not accurately convey the ways early scribes actually wrote. In addition to challenging this “Standard Model” of Syriac scripts, the project illustrates how large data sets, digital analysis, and visual analytics can help researchers address key philological and historical problems

Using Participatory Scenarios to Stimulate Social Learning for Collaborative Sustainable Development

Interdependent human and biophysical systems are highly complex and behave in unpredictable and uncontrollable ways. Social and ecological challenges that emerge from this complexity often defy straightforward solutions, and efforts to address these problems will require not only scientific and technological capabilities but also learning and adaptation. Scenarios are a useful tool for grappling with the uncertainty and complexity of social-ecological challenges because they enable participants to build adaptive capacity through the contemplation of multiple future possibilities. Furthermore, scenarios provide a platform for social learning, which is critical to acting in the face of uncertain, complex, and conflict-laden problems. We studied the Minnesota 2050 project, a collaborative project through which citizens collectively imagined future scenarios and contemplated the implications of these possibilities for the adaptability of their social and environmental communities. Survey and interview data indicate that these participatory scenario workshops built and strengthened relationships, enhanced participants’ understanding of other perspectives, and triggered systemic thinking, all of which is relevant to collective efforts to respond to social-ecological challenges through sustainable development activities. Our analysis shows that participatory scenarios can stimulate social learning by enabling participants to engage and to discuss options for coping with uncertainty through collaborative actions. Such learning can be of value to participants and to the organizations and decisions in which they are engaged, and scenario processes can be effective tools for supporting collaborative sustainable development efforts

Set1/COMPASS repels heterochromatin invasion at euchromatic sites by disrupting Suv39/Clr4 activity and nucleosome stability.

Protection of euchromatin from invasion by gene-repressive heterochromatin is critical for cellular health and viability. In addition to constitutive loci such as pericentromeres and subtelomeres, heterochromatin can be found interspersed in gene-rich euchromatin, where it regulates gene expression pertinent to cell fate. While heterochromatin and euchromatin are globally poised for mutual antagonism, the mechanisms underlying precise spatial encoding of heterochromatin containment within euchromatic sites remain opaque. We investigated ectopic heterochromatin invasion by manipulating the fission yeast mating type locus boundary using a single-cell spreading reporter system. We found that heterochromatin repulsion is locally encoded by Set1/COMPASS on certain actively transcribed genes and that this protective role is most prominent at heterochromatin islands, small domains interspersed in euchromatin that regulate cell fate specifiers. Sensitivity to invasion by heterochromatin, surprisingly, is not dependent on Set1 altering overall gene expression levels. Rather, the gene-protective effect is strictly dependent on Set1's catalytic activity. H3K4 methylation, the Set1 product, antagonizes spreading in two ways: directly inhibiting catalysis by Suv39/Clr4 and locally disrupting nucleosome stability. Taken together, these results describe a mechanism for spatial encoding of euchromatic signals that repel heterochromatin invasion

Molecular Recognition of Insulin by a Synthetic Receptor

The discovery of molecules that bind tightly and selectively to desired proteins continues to drive innovation at the interface of chemistry and biology. This paper describes the binding of human insulin by the synthetic receptor cucurbit[7]uril (Q7) in vitro. Isothermal titration calorimetry and fluorescence spectroscopy experiments show that Q7 binds to insulin with an equilibrium association constant of 1.5 × 106 M−1 and with 50−100-fold selectivity versus proteins that are much larger but lack an N-terminal aromatic residue, and with \u3e1000-fold selectivity versus an insulin variant lacking the N-terminal phenylalanine (Phe) residue. The crystal structure of the Q7·insulin complex shows that binding occurs at the N-terminal Phe residue and that the N-terminus unfolds to enable binding. These findings suggest that site-selective recognition is based on the properties inherent to a protein terminus, including the unique chemical epitope presented by the terminal residue and the greater freedom of the terminus to unfold, like the end of a ball of string, to accommodate binding. Insulin recognition was predicted accurately from studies on short peptides and exemplifies an approach to protein recognition by targeting the terminus

Animal Toxicity of Hairpin Pyrrole-Imidazole Polyamides Varies with the Turn Unit

A hairpin pyrrole-imidazole polyamide (1) targeted to the androgen receptor consensus half-site was found to exert antitumor effects against prostate cancer xenografts. A previous animal study showed that 1, which has a chiral amine at the α-position of the γ-aminobutyric acid turn (γ-turn), did not exhibit toxicity at doses less than 10 mg/kg. In the same study, a polyamide with an acetamide at the β-position of the γ-turn resulted in animal morbidity at 2.3 mg/kg. To identify structural motifs that cause animal toxicity, we synthesized polyamides 1–4 with variations at the α- and β-positions in the γ-turn. Weight loss, histopathology, and serum chemistry were analyzed in mice post-treatment. While serum concentration was similar for all four polyamides after injection, dose-limiting liver toxicity was only observed for three polyamides. Polyamide 3, with an α-acetamide, caused no significant evidence of rodent toxicity and retains activity against LNCaP xenografts

Simulating the effect of perennialized cropping systems on nitrate-N losses using the SWAT model

Several newly released crop varieties, including the perennial intermediate wheatgrass (grain marketed as Kernza®), and the winter hardy oilseed crop camelina, have been developed to provide both economic return for farmers and reduced nutrient losses from agricultural fields. Though studies have indicated that these crops could reduce nitrate-nitrogen (N) leaching, little research has been done to determine their effectiveness in reducing nitrate-N loading to surface waters at a watershed scale, or in comparing their performance to more traditional perennial crops, such as alfalfa. In this study, nitrate-N losses were predicted using the Soil and Water Assessment Tool (SWAT) model for the Rogers Creek watershed located in south-central Minnesota, USA. Predicted looses of nitrate-N under three perennialized cropping systems were compared to losses given current cropping practices in a corn (Zea mays L.)-soybean (Glycine max L. Merr.) rotation. The perennialized systems included three separate crop rotations: intermediate wheatgrass (IWG) in rotation with soybean, alfalfa in rotation with corn, and winter camelina in rotation with soybean and winter rye. Model simulation of these rotations required creation of new crop files for IWG and winter camelina within SWAT. These new crop files were validated using measured yield, biomass, and nitrate-N data. Model results show that the IWG and alfalfa rotations were particularly effective at reducing nutrient and sediment losses from agricultural areas in the watershed, but smaller reductions were also achieved with the winter camelina rotation. From model predictions, achieving regional water-quality goals of a 30% reduction in nitrate-N load from fields in the watershed required converting approximately 25, 34, or 57% of current corn-soybean area to the alfalfa, IWG, or camelina rotations, respectively. Results of this study indicate that adoption of these crops could achieve regional water quality goals