Peptide and protein sequences are most commonly represented as a strings: a series of letters selected from the twenty character alphabet of abbreviations for the naturally occurring amino acids. Here, we experiment with representations of small peptide sequences that incorporate more physiochemical information. Specifically, we develop three different physiochemical representations for a set of roughly 700 HIV–I protease substrates. These different representations are used as input to an array of six different machine learning models which are used to predict whether or not a given peptide is likely to be an acceptable substrate for the protease. Our results show that, in general, higher–dimensional physiochemical representations tend to have better performance than representations incorporating fewer dimensions selected on the basis of high information content. We contend that such representations are more biologically relevant than simple string–based representations and are likely to more accurately capture peptide characteristics that are functionally important. / Singapore-MIT Alliance (SMA)

Poly(lactic acid) (PLA) is a polymer chain consisting of repeating units of lactic acid (LA) used in various biomedical applications because of its biocompatible features. It is commonly used as a subdermal filler and constitutes as the main ingredient in SculptraR, which is a collagen regenerating filler used to treat lipoatrophy of the cheeks or to rejuvenate the skin. The presence of macrophages triggers a foreign body reaction in response to PLA, which in turn prompts fibroblasts to gradually increase collagen fibers in the dermis. This literature study investigates how physical properties such as Mw, morphology, stereochemistry as well as chemical properties, influence the biological response and degradation of PLA. Additionally, a comparison of other bio stimulants, substituents and copolymers were performed. The aim of this study was constructed in collaboration with Galderma. All aspects that were taken into consideration affected the biological response and degradation to some extent. The degradation of the PLLA microspheres has a noticeable correlation to the biological immune response. An increase in the Mw and degree of crystallinity results in a decrease in degradation rate. Morphology greatly influences the immune response and particle size is vital for the degradation as well as biostimulation. The most suitable stereoisomer of PLA is the (L)-form based on both biological response and degradation. Decomposition of PLLA varies depending on the Mw which is affected by the pH of the surrounding environment. Compared to other substances used in biodegradable products, PLLA is regarded as the most auspicious for a durable result. PDLLA has desirable biological responses but is degraded too fast. PDLA is not suitable as a dermal filler due to its inflammatory response and bad collagen regeneration.

Wetlands are one of the most productive ecosystems in the world, providing a range of services, including: water quality improvement, flood mitigation, erosion control, habitat, and carbon storage. It is estimated that Tennessee has lost 60% of its original 2 million acres of pre-European settlement wetlands. Recently, increased funding has been made available for wetland restoration and expansion. In response, the Cherokee National Forest has proposed a range of wetland restoration actions within the Paint Creek Watershed to expand and restore some of the existing bogs and fens, including the Cutshaw Bog, a 163,864 m2 wetland located 32 km south of Greeneville, TN. The U.S. Forest Service has proposed a new expanded wetland boundary to result from restoration efforts. However, to assess the potential for success, current wetland indicators based on soil color, texture, depth, drainage, sulfide materials, and iron concentrations were examined. Sampling locations were identified by overlaying a grid, composed of 64 cells, each 40.5 meter by 40.5 meter in size. Soil cores were extracted up to a depth of 0.6 meters from each sampling cell and evaluated in situ for hydric soil properties using the Eastern Mountains and Piedmont Army Corps of Engineers Wetlands Delineation Manual. Soil physical (texture, bulk density, moisture content) and chemical (pH, cation exchange capacity, % base saturation, Nitrogen, Bray II Phosphorus, Iron, Zinc, and Total Carbon Content) properties were evaluated in the laboratory. Results indicated 47% of samples taken within the proposed wetland expansion area currently have hydric soil characteristics and were located along drainage lines. Presence of hydric soils was correlated with soil physicochemical properties including bulk density, moisture content, sulfur and phosphorus concentrations, iron, and other metals. Statistical analyses for the northern section and southern section of the bog were completed separately, as they were physically divided by a French drain structure. Logistic regression models were developed using properties most strongly correlated with the presence of hydric soil. For the northern section, bulk density and iron were retained in the model, while for the southern section, iron was retained. A spatial model for the presence of hydric soil was developed by spatially interpolating the covariates through kriging. Next, a probability map was created from the logistic regression equation with raster math in ArcGIS Pro. Results indicate that Cutshaw Bog’s area cannot be expanded to the original proposed boundary provided by the US Forest Service and a new recommended boundary was delineated from the probability map. The results of this data driven approach will assist the Forest Service in targeted wetland restoration efforts at the Cutshaw Bog.