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)

Many plants require exposure to low temperature for a certain period during each year. This was determined more than a century ago. Understanding this phenomenon, known as the rest period, is part of a larger problem of understanding the factors which determine the ability of an organism to grow. The property of rest is ultimately a property of the actively growing cells, rather than that of the cells involved with protection and support.

The effects of controlled atmosphere on the metabolism of Golden Delicious and Rome Beauty apples, Anjou pears, and Lambert and Bing cherries were studied with respect to changes caused in the normal metabolic functions carried on during storage of these fruits. Atmospheres consisting of 1.5 per cent CO2 and 2.5 per cent O2 for the apples and pears and 10.5 per cent CO2 and 2.5 per cent O2 for the cherries were employed. Fungi of the strains Botrytis alli, Rhizopus nigricans, and Penicillium expansum were subjected to controlled atmospheres at 21° C to determine the toxic effect of CA. The fungi were grown on agar plates instead of fruit to prevent bias, such as condition of the fruit. Periodically, fruit was taken directly from the storage treatments and analyzed for CO2 evolution, for total and reducing sugars, organic acids, amino acids, and cytochrome c oxidase. Fruits were also taken from the storage treatments and held for a specific time at 15° C before analysis. The CA used in this experiment had an inhibitory effect on the fungi that were used. Botrytis alli and Penicillium expansum were particularly susceptible. It was found the height of the mycelial mat was less, the mycelium growth was less, and while sporulation was not eliminated, it was severely retarded. Combinations of CA and lowered temperatures should attain a high degree of fungal control. The results showed that CA had an inhibitory effect on the metabolic system of stored fruits. The specific areas of metabolic inhibition are not known exactly. This inhibition does not appear to be of a permanent nature as shown by the post storage analysis. Any differences that occurred in the CA stored fruit as contrasted to the fruit from the conventional stored fruit appeared to be able to correct themselves once they were removed from the CA.

The extent and nature of physio-chemical changes that take place in detached leaves after harvest and during storage have been reviewed and discussed by Osborne (1962) and Rogers (1955). These changes include loss of moisture (Wittwer et al., 1962), chlorophyll degredation (Person et al., 1957), Protein loss (Thimann and Manmahan, 1960), and result in subsequent appearance of the visual manifestations of senescence of plant tissues. As lettuce, like most leafy vegetables, deteriorates rapidly and steadily after harvest. Loss of quality is inevitable and can only be minimized by rapid handling and with the best possible storage conditions (Pratt et al., 1954). In recent years, abundant work has been done to delay senescence by the use of various chemicals. Among the investigated chemicals, kinetin (6-furfurylarninopurine) and its related c ompounds show some promise. Van Overbeek et al. (1941) reported a potent new growthpromoting factor (kinetin) in coconut milk. This chemical is active in causing many of the growth reactions of c oconut milk at exceedingly small dosages. Subsequently several arninopurine compounds were synthesized. One of which is SD 4901 (Verdan), N6-benzyladenine, an experimental senescence inhibitor, was developed by Shell Development Company, Modesto, California in 1960. Many reports showed that this chemical is capable of delaying senescence of plant tissues on the basis of restoring protein molecules and respiration inhibition. On the other hand, others have shown stimulation of respiration and delaying of senescence. Paucity of scientific literature on the stability of those chemicals on leafy vegetables gave impetus to a study of the comparative influence of pre- and post-harvest applications of 6-furfurylaminopurine and N6-benzyladenine as related to successive harvest times. Such studies may have considerable economic bearing upon storing and shipping leafy vegetables to distant markets. This thesis presents effects of different concentrations (5, 10, and 20 ppm.) of pre- and post-harvest applications of 6-furfurylaminopurine and N6-benzyladenine as related to three successive harvest times (at one week intervals) on chlorophyll content, moisture content, total nitrogen, insoluble and soluble nitrogen, oxygen uptake, 0 and co2 production during storage (at 40 Fo and 85 percent RH) of "Great Lakes" variety of lettuce.

The post-harvest physiology of sugarbeet (Beta vulgaris) roots was studied during controlled atmosphere (CA) storage at 35° and 50°F. Zero, 3, 6 and 10% carbon dioxide and 5% oxygen concentrations were employed to investigate the most beneficial concentrations of gases. Under the experimental conditions beets were stored successfully for 200 days. The maximum beneficial effects of CA were observed under 6% carbon dioxide and 5% oxygen at 35°F. Regardless of storage temperatures , sucrose retention was highest in the beets stored under CA, compared to conventional refrigeration (CR). Other beneficial effects include less hydrolysis of sucrose to reducing sugars and a decrease in raffinose accumulation. Fungal growth and sprouting were also inhibited significantly, under CA. In the second phase of the studies, investigations were conducted on sugarbeets to study the effects of different levels of nitrogen fertilizer on the optimum CA storage at 40°F. Regardless of the level of nitrogen fertilization, the beets stored under CA demonstrated beneficial effects as described earlier. In addition, respiration, measured on the whole beets, and amino nitrogen content of the beets were lower in the CA-stored beets than those stored under CR. Accumulation of citric acid and succinic acid was significant in the CA-stored beets.

River water is used for a range of purposes, for example irrigation, laundry, hygiene, mining of sand, as drinking water and for disposal of wastes and wastewater. These anthropogenic activities, along with agriculture and the local climate and geology will have effects on the water quality, and by extension the people living in the area. This study intends to evaluate the water quality of Likangala River, which is a perennial river in southern Malawi, during hot dry season linking it to the activities present in the direct vicinity of the urban segment of the river. A small land use survey was carried out, and eight points for water sampling chosen for analysis of a set of physio-chemical water quality parameters. Also an estimate of the water discharge of the time was made. It was found that most parameters were within the guidelines for drinking water set up by WHO (2011) and Malawi Bureau of Standards (MBS, 2008), although turbidity, manganese, iron, chromium and lead showed elevated levels. Some, but not all, parameters showed a trend with low values upstream the city and higher values downstream (except pH with a inverse trend), and almost all parameters were significantly higher in the effluents from the Zomba Sewage Works, and also directly afterwards. / Flodvatten används för en rad olika ändamål, exempelvis bevattning, tvätt, hygien, utvinning av sand, som dricksvatten och för avyttrande av avfall och avloppsvatten. Dessa mänskliga verksamheter, tillsammans med effekter av jordbruk samt det lokala klimatet och geologin kommer att påverka vattenkvaliteten, och i förlängningen de människor som bor i området. Denna studie avser att utvärdera vattenkvaliteten i Likangala, som är en flod i södra Malawi, under heta torrperioden och koppla denna till de verksamheter som finns i dess direkta närhet längs den urbana sträckningen av floden. En liten kartläggning av markanvändning genomfördes, och åtta platser för vattenprovtagning valdes ut för analys av ett antal fysio-kemiska vattenkvalitets- parametrar. Också en uppskattning av vattenföring gjordes. Det visade sig att de flesta parametrar var inom riktlinjerna för dricksvatten som inrättats av WHO (2011) och Malawi Bureau of Standards (MBS, 2008), även om turbiditet, mangan, järn, krom och bly visade förhöjda halter. Vissa, men inte alla, parametrar visade en trend med låga värden uppströms staden och högre värden nedströms (förutom pH med en inverterad trend), och nästan alla parametrar var betydligt högre i spillvattnet från Zomba vattenreningsverk, och även direkt efteråt.

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.

Carrots (Daucus carota L. cv. Royal Chantenay) and sweet corn vi (Zea mays L. cv. Iochief) were grown rm the Utah State University's Greenville farm in 1969 and 1970. The soil was fumigated with Telone (a mixture of 1, 3-dichloropropene and other chlorinated hydrocarbons) at the rates of 10, 20, and 30 gal/acre and Nemagon (1, 2-dibromo-3-chloropropane) at the rates of 1, 2, and 3 gal/acre one week before planting. Samples of uniformly mature carrot roots were taken for the studies of total carotenes, β-carotene, total and reducing sugars, respiration, and ultrastructural changes; and those of sweet corn seeds for the studies of total carotenoids , starch, total sugar, and total nitrogen changes. Compared to the controls, carrots grown on fumigated soil had a significantly higher content of total carotenes, β-carotene, and total sugars, and a lower rate of respiration. The electron microscopic study indicated that the carrots from Telone (30 gal/acre) and Nemagon (3 gal/acre) fumigated soil had larger chromoplasts that contained more globuli and crystals than those of the controls. The soil fumigations with Telone and Nemagon also brought about the increase in total carotenoid content in sweet corn seeds.

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.