Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Ethnobotanical Study of Medicinal Plants Used to Treat Human Diseases in Berbere District, Bale Zone of Oromia Regional State, South East Ethiopia

This paper reports an ethnobotanical study that focused on the traditional medicinal plants used by local communities to treat human diseases. Ethnobotanical study of medicinal plants was carried out from June 25 to September 5, 2015, in Berbere district of Oromia region, Ethiopia. The study focused on documentation of medicinal plants used to treat various human diseases in the study area. Ethnobotanical data were collected using semistructured interviews, group discussion, guided field walks, and observations with participants. Preference ranking, paired comparison, direct matrix ranking, and informant consensus factors (ICF) were used to analyze the importance of some plant species. A total of 70 medicinal plants, distributed in 56 genera and 46 families, were collected and identified. Plant family with the highest medicinal plants in the study area used for various diseases treatment was Euphorbiaceae (11.4%). The result of growth form analysis showed that shrubs constituted the highest proportion of medicinal plants (48.6%). Roots, 43 (44.8%), were the most frequently utilized plant parts for preparation of traditional herbal medicines. Crushing was a widely used mode of preparation of traditional remedies where oral administration (37.5%) was the dominant route. The highest informants consensus factor (ICF) values were linked to gonorrhea and syphilis disease (0.95); the lowest was linked with external parasites and wound (0.69). Local people in the study area possess traditional knowledge of medicinal plants to treat various human ailments; however, agricultural expansion and disinterest of young generation became the major threat to medicinal plants. It is, therefore, necessary to preserve this indigenous knowledge on traditional medicines by proper documentation, identification of plant species used, and herbal preparation. To save medicinal plants from further loss, involving local communities in cultivation of the most utilized medicinal plants is recommended

Experimental Evaluation on Comparative Performance of Native Plant Species in Removing Turbidity and Microbial Load for Household Water Treatment

Unsafe drinking water is a paramount concern because of the fact that, 75% of all diseases in developing countries are arising from polluted drinking water especially in rural parts of developing countries. This work investigates on comparative performance of native plant species in removing turbidity and microbial load as compared to alum and chlorine for household water treatment. Water treatment using Maerua subcordata (Gilg) De Wolf and Moringa stenopetala (Bakj) Cufod were able to achieve appreciable removal efficiency in both turbidity and microbial load at an optimum dose range of 0.01gm/L to 0.03 gm/L in synthetic water and natural surface water samples. Plant coagulants showed relatively lower removal efficiency (≈70%) as compared to alum (≈80%) at low turbidity (20 NTU) in synthetic water. However, in natural water samples of low turbidity, plant coagulants showed high rate of turbidity removal efficiency (≈90%) like that of alum. Plant coagulants can also achieve maximum turbidity removal (≈97%) like that of alum in medium turbidity level (200 NTU) in both natural and synthetic water samples. The experimental result revealed that plant coagulants were able to meet World Health Organization standards of drinking water quality (< 5 NTU) in terms of turbidity. The microbial reduction experiment also revealed that plant coagulants can effectively disinfect water at low turbidity but becomes less potent disinfectant as turbidity increases. Key words:Coagulation, Disinfection, Household water treatment, Native plants, Turbidit

Assessment of the quality of drinking water in storage tanks and its implication on the safety of urban water supply in developing countries

Abstract Background Water quality problems are one of the manifestations of poverty and most developing countries including Ethiopia suffering a lot of health problems associated with consumption of contaminated water. Although communities living in urban areas of Ethiopia have access to piped water supply, cross-contamination in the distribution system and unsafe storage are the major source of water borne diseases hence they are mostly overlooked by water professionals. Results All water samples collected from drinking water storage tanks were positive for total coliforms and faecal coliforms. The result of this study showed that the drinking water was microbially contaminated in all sampling points. The level of microbial contamination increased from before entering the storage tank to after leaving the storage tank indicating that the presence of leakage in the distribution system and contamination at the storage tanks. The turbidity was found in the safe water quality range (2.1–2.9 NTU). Conclusion The current study indicated that all water samples were bacteriologically contaminated and none of them met the WHO maximum permissible limit of drinking water quality. The unsafe piped-water supply was attributed to both leakage and contamination in the distribution system or unsafe storage. Thus, detail risk assessment should be conducted from treatment to distribution including storage and safe handling of water at the point of use in order to provide complete intervention strategies in tackling waterborne diseases

Medicinal Plants Used for Treatment of Diarrhoeal Related Diseases in Ethiopia

This paper presents a review of relevant antidiarrhoeal medicinal plants based on the fundamental knowledge accumulated by indigenous people of Ethiopia. The review includes an inventory carried out on the phytochemical and pharmacological analysis of plant species used in the treatments of diarrhoeal diseases. This study is based on a review of the literature published in scientific journals, books, theses, proceedings, and reports. A total of 132 medicinal plants used by local people of Ethiopia are reported in the reviewed literature. Herbs (43.6%) were the primary source of medicinal plants, followed by trees (27%). Some findings include the predominance of leaf material used (78%), as well as the frequent use of crushing of the plant parts (38%) as a mode of preparation. This study demonstrates the importance of traditional medicines in the treatment of basic human ailments such as diarrhoeal diseases in Ethiopia. Baseline information gaps were observed in different regions of Ethiopia. Thus, documentation of the knowledge held by other regions of Ethiopia that have so far received less attention and urban ethnobotany is recommended for future ethnobotanical studies. In addition, phytochemical studies are recommended mainly on frequently utilized medicinal plants for treatment of diarrhoeal diseases which can serve as a basis for future investigation of modern drug development. Although societies in Ethiopia have long used medicinal plants for diarrhoeal diseases treatment, it is also a good practice to perform toxicological tests

Solar disinfection potentials of aqua lens, photovoltaic and glass bottle subsequent to plant-based coagulant: for low-cost household water treatment systems

Abstract Unaffordable construction cost of conventional water treatment plant and distribution system in most developing countries makes difficult to provide safe and adequate water for all households, especially for the rural setup. Water treatment at the source can be the best alternative. Solar disinfection is one alternative among point of use treatments. In this study, aqua lens, photovoltaic box and glass bottle were used subsequent to plant coagulants to evaluate microbial reduction potentials. Laboratory- and field-based experiments were conducted from May to August 2016. The Escherichia coli, total coliforms and heterotrophic plate counts were used as indicator organisms. The result indicated that aqua lens (AL), photovoltaic box (PV) and glass bottle (GB) have high inactivation rate subsequently almost for all indicator organisms in short solar exposure time. Total coliforms were inactivated in AL (SD = 15.8 °C, R 2 = 0.92) followed by PV inactivation temperature association (SD = 11.6 C, R 2 = 0.90), and the GB concentrator was inactivated (SD = 10.9 °C, R 2 = 0.70) at turbidity level of 3.41 NTU. As the study indicated, aqua lens coupled with Moringa oleifera coagulant can be an effective with minimum cost for household water treatment system. The study also concludes heterotrophic bacteria were more resistant than other types of bacteria in SODIS with similar exposure time

Depth profile of reservoir water quality in the Southwest of Ethiopia

The objective of this research was to investigate the variation of water quality parameters at different depths of the Gilgel Gibe I reservoir in Oromia Jimma zone during wet seasons. Five stations within the reservoir were selected, and water quality parameters were determined at four different depths (surface, 5 m, 10 m, and 15 m). Water quality parameters were analyzed on-site using a HACH, HQ40d portable multi-meter, and turbidity was measured using Wag tech turbidity meter and in the laboratory using the standard method. Comparison of water quality parameters among depths were conducted using one-way ANOVA and Tukey's pairwise comparisons with 5% significance level. The probable contributing source of the investigated physicochemical water quality parameters at different depth was identified using Principal components analysis. The results show that depth wise except for total suspended solids (TSS), total dissolved solids (TDS), total phosphorus (TP) and soluble reactive phosphorus (SRP) the rest showed statistically significant difference at p < 0.05 level. Negative correlations were found between depth and dissolved oxygen (DO), water temperature, pH, nitrate (N03-) and chlorophyll a (Chl.a) while positive correlations were found between electrical conductivity (EC), biochemical oxygen demand (BOD5), turbidity and N03-. The study revealed that the release of nutrients associated with increased concentration of BOD5 at the bottom depth caused low concentration of dissolved oxygen due to oxygen consumption. This was further aggravated through the decomposition of organic matter, indicating organic pollution resulting from runoff from the catchment. The presence of dense masses of blue-green algae in the pelagic zone of Gilgel Gibe I reservoir suggested the presence of ample nutrients for its blooming and significant reduction of water quality, indicating possible eutrophic conditions. Therefore, catchment management is required to protect aquatic life and the reservoir function as a whole from reservoir water quality degradation

Ethnobotanical study of wild edible plants in Arsi Robe district of East Arsi Zone, Ethiopia

Abstract Background Wild edible plants (WEPs) are usually considered to constitute all plant resources that are neither cultivated nor domesticated but are used as nutritional supplements by local people. WEPs play a vital role in ensuring food and livelihood security for countless families and communities around the world. The objective of the study was to assess and document wild edible plants used by communities in the Arsi Robe district as food. Methods Semi-structured interviews, market surveys, and guided field walks were employed as data collection tools. The data were analyzed using preference ranking, direct matrix ranking, and Jaccard’s similarity index. Results The present study revealed various types of wild edible plants consumed by local communities in the Arsi Robe district of the East Arsi Zone. This could be justified by the documentation of 36 different wild edible plants in the study area. These WEPs belong to 31 genera and 25 families. Most of the growth forms of the edible wild plants in the district were shrubs (16, 44.44%) and trees (14, 38.88%). Amaranthus caudatus and Bridelia micrantha are the most preferred WEPs in the study area. The finding of the study also revealed that Lepidotrichilia volkensii and Premna schimperi are among the novel WEPs that had not before been documented as food items in other areas. Olea europaea subsp. cuspidata, Ficus sycomorus, Cordia africana, and Ficus sur are species with multiple uses. Agricultural expansion, charcoal production, the construction of different materials, making agricultural tools, deforestation, and other factors were the top prioritized threats affecting the abundance and diversity of wild edible plants. Conclusion Along with the sustainable utilization and conservation of the existing WEPs of the study district, priority should be given to the urgent collection, domestication, and cultivation of multiuse wild edible plant species such as Olea europaea subsp. cuspidata, Ficus sycomorus, Cordia africana, and Ficus sur in the study area