A rapid-assessment survey of the irrigation component of the Anuradhapura Dry-Zone Agricultural Project (ADZAP)

Irrigation / Farmer managed irrigation systems / Surveys / Tank irrigation / Farmer-agency interactions / Settlement / Policy / Sri Lanka / Anuradhapura

Contrastive Deep Encoding Enables Uncertainty-aware Machine-learning-assisted Histopathology

Deep neural network models can learn clinically relevant features from millions of histopathology images. However generating high-quality annotations to train such models for each hospital, each cancer type, and each diagnostic task is prohibitively laborious. On the other hand, terabytes of training data -- while lacking reliable annotations -- are readily available in the public domain in some cases. In this work, we explore how these large datasets can be consciously utilized to pre-train deep networks to encode informative representations. We then fine-tune our pre-trained models on a fraction of annotated training data to perform specific downstream tasks. We show that our approach can reach the state-of-the-art (SOTA) for patch-level classification with only 1-10% randomly selected annotations compared to other SOTA approaches. Moreover, we propose an uncertainty-aware loss function, to quantify the model confidence during inference. Quantified uncertainty helps experts select the best instances to label for further training. Our uncertainty-aware labeling reaches the SOTA with significantly fewer annotations compared to random labeling. Last, we demonstrate how our pre-trained encoders can surpass current SOTA for whole-slide image classification with weak supervision. Our work lays the foundation for data and task-agnostic pre-trained deep networks with quantified uncertainty.Comment: 18 pages, 8 figure

Groundwater quality and antibiotic resistance of coliform bacteria in Wilgamuwa, an area of Chronic Kidney Disease of unknown etiology (CKDu) in Sri Lanka

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Antimicrobial activity of some Sri Lankan Rubiaceae and Meliaceae

Ninety solvent extracts (n-hexane, dichloromethane and methanol) obtained from the leaves, bark and stem of 13 Sri Lankan Rubiaceae and two Sri Lankan Meliaceae plants have been screened for antibacterial and antifungal activities. Morinda tinctoria, Mussaenda frondosa, Psychotria gardneri and Psychotria stenophylla displayed the widest spectrum of antibacterial activity

Clinico-pathological factors influencing the recurrence free interval of patients with recurrent breast cancer

Objectives: Clinico-pathological factors affect the prognosis of breast cancer (BC) reflecting the heterogeneity of the disease. Following initial treatment, there is an ongoing risk of recurrence. The influence of these prognostic factors on the time taken to develop recurrence is not well established. This study was designed to determine the effect of clinic-pathological factors on the recurrence free interval (RFI) of BC patients with recurrent disease.Methods: This retrospective study included BC patients who had sought the immunohistochemistry laboratory services of our unit from May 2006 to December 2012. Mean follow up time was 45±23 months. All BC patients who had recurrences (loco-regional and distant metastasis) during the follow up period were enrolled. RFI was measured from the date of first therapeutic intervention to the date of confirmation of recurrence. Chi-square test was used for analysis.Results: Out of 944 BC patients, 188(mean age 50±11 years), had recurrences (loco-regional =35, distant metastasis =153). More than 50% of them had recurrence within 24 months of initial treatment (local=18/35 and distant=81/153). Mean RFI was 33±21 months for oestrogen receptor (ER)/progesterone receptor (PR) positive BC and 22±16 months for ER/PR negative BC. ER/PR positive BCs had a significant upward trend in developing recurrences over time (χ2 trend<0.001) while the rest had a downward trend. Other clinico-pathological factors were not associated with RFI. Majority (49/53) of the ER/PR positive BC patients had received hormone therapy and 179/188 BC patients had received chemotherapy.Conclusions: ER/PR positive BC patients develop late recurrences while hormone receptor negative patients develop early recurrences depicting late and early treatment failure in respective groups

Synergistic activity of polarised osteoblasts inside condensations cause their differentiation

Condensation of pre-osteogenic, or pre-chondrogenic, cells is the first of a series of processes that initiate skeletal development. We present a validated, novel, three-dimensional agent-based model of in vitro intramembranous osteogenic condensation. The model, informed by system heterogeneity and relying on an interaction-reliant strategy, is shown to be sensitive to 'rules' capturing condensation growth and can be employed to track activity of individual cells to observe their macroscopic impact. It, therefore, makes available previously inaccessible data, offering new insights and providing a new context for exploring the emergence, as well as normal and abnormal development, of osteogenic structures. Of the several stages of condensation we investigate osteoblast 'burial' within the osteoid they deposit. The mechanisms underlying entrapment - required for osteoblasts to differentiate into osteocytes - remain a matter of conjecture with several hypotheses claiming to capture this important transition. Computational examination of this transition indicates that osteoblasts neither turn off nor slow down their matrix secreting genes - a widely held view; nor do they secrete matrix randomly. The model further reveals that osteoblasts display polarised behaviour to deposit osteoid. This is both an important addition to our understanding of condensation and an important validation of the model's utility

Meta-analysis of nature conservation values in Asia & Oceania: Data heterogeneity and benefit transfer issues

We conduct a meta-analysis (MA) of around 100 studies valuing nature conservation in Asia and Oceania. Dividing our dataset into two levels of heterogeneity in terms of good characteristics (endangered species vs. nature conservation more generally) and valuation methods, we show that the degree of regularity and conformity with theory and empirical expectations is higher for the more homogenous dataset of contingent valuation of endangered species. For example, we find that willingness to pay (WTP) for preservation of mammals tends to be higher than other species and that WTP for species preservation increases with income. Increasing the degree of heterogeneity in the valuation data, however, preserves much of the regularity, and the explanatory power of some of our models is in the range of other MA studies of goods typically assumed to be more homogenous (such as water quality). Subjecting our best MA models to a simple test forecasting values for out-of-sample observations, shows median (mean) forecasting errors of 24 (46) percent for endangered species and 46 (89) percent for nature conservation more generally, approaching levels that may be acceptable in benefit transfer for policy use. We recommend that the most prudent MA practice is to control for heterogeneity in regressions and sensitivity analysis, rather than to limit datasets by non-transparent criteria to a level of heterogeneity deemed acceptable to the individual analyst. However, the trade-off will always be present and the issue of acceptable level of heterogeneity in MA is far from settle

Catch Diversity of Small Scale Lobster Fishery in Southern Coast of Sri Lanka

The lobster fishery is one of the well-established, highly valued commercial fisheries on the Southern coast of Sri Lanka. There are five spiny lobster species, Panulirus homarus, P. longipes, P. ornatus, P. versicolor and P. penicillatus are recorded in the Southern coast of Sri Lanka. However, the heavy fishing pressure and other anthropogenic interventions have caused a significant depletion of some of these species. Therefore, in order to identify the vulnerability of the lobster species, we studied the species, gender and sexual maturity compositions of the lobster catch with the data collected from nine different lobster landing sites along the southern coast of Sri Lanka during 2019 and 2020. Minitab and MS Excel software were used for the descriptive statistical analysis. According to the results, the dominant species in the sampled landings was P. homarus, with the average percentage of 73.16% in 2019 and 84.65% in 2020. However, least abundant P. ornatus species’ average percentages were 0.74% in 2019 and 0.27% in 2020. Moreover the results reveals the male:female 1:1 sex ratio of the lobster catches as 1:0.9 in 2019 and 1:0.89 in 2020. Most importantly, among all females, there were 43.01% in 2019 and 37.31% in 2020 percentages borne eggs while 48.53% in 2019 and 47.03% in 2020 percentage of females were identified with tar spots. Therefore, considerable caught of tar spotted and egg bearing female lobsters might be a major cause of lobster stock depletion in Southern coast of Sri Lanka. Thus present study would be a preliminary guide for the future studies on sustainable lobster fishery management approach. Keywords: Lobsters fishery, Southern coast, Panulirus homarus, Tar spots, Sri Lank