The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods.

Groundwater arsenic contamination has caused a significant public health burden in lowland regions of Nepal. For arsenic mitigation purposes, the Kanchan Arsenic Filter (KAF) was developed and validated for use in 2003 after pilot studies showed its effectiveness in removing arsenic. However, its efficacy in field conditions operating for a long period has been scarcely observed. In this study, we observe the efficacy of KAFs running over 6 months in highly arsenic-affected households in Nawalparasi district. We assessed pair-wise arsenic concentrations of 62 randomly selected household tubewells before filtration and after filtration via KAFs. Of 62 tubewells, 41 had influent arsenic concentration exceeding the Nepal drinking water quality standard value (50 μg/L). Of the 41 tubewells having unsafe arsenic levels, KAFs reduced arsenic concentration to the safe level for only 22 tubewells, an efficacy of 54%. In conclusion, we did not find significantly high efficacy of KAFs in reducing unsafe influent arsenic level to the safe level under the in situ field conditions.

A significant public health problem due to exposure to arsenic via groundwater in communities of lowland Terai region of Nepal has issued forth need to assess the exposure status and factors associated with arsenicosis. We observed arsenical dermal manifestations and collected and assessed total arsenic content in tubewell water, urine, and hair samples of study subjects at arsenic affected communities in Nawalparasi district of Nepal. The explanatory variables associated with arsenicosis were elevated arsenic in tubewell, male gender and increased age (P < 0.05). 67% (73/109) and 66% (77/117) of subjects exceeded the normal urinary and hair arsenic levels respectively. Among them 52% (57/109) and 47% (55/117) exceeded normal urinary and hair arsenic levels having no arsenical dermal manifestations. Males and symptomatic cases had significantly higher hair arsenic levels (P < 0.05). We also observed significant positive correlation of both urine and hair arsenic levels to tubewell arsenic levels (r = 0.27, 0.37, P < 0.01) and negative correlation of urine arsenic levels with the age of the subjects (r = -0.18, P = 0.06). We conclude that elucidating factors associated with arsenicosis could be of prime importance in intervention and preventive measures. In arsenic affected communities of Nepal exposure to arsenic is still a major problem despite mitigation efforts and the potential for sub-clinical effects in exposed population is high.

Community-based information on antibiotic susceptibility of urinary bacteria is useful in clinical practice, including empiric therapy. Owing to evidence of coselection of metal and antibiotic resistance, there is growing concern on testing of such selective pressure in clinical as well as environmental bacterial isolates. We examined arsenic tolerance and antibiotic resistance in urinary isolates and their possible coselection among arsenic-exposed subjects. Urinary arsenic levels were assessed by atomic absorption spectrophotometer. Antibiotic resistance and arsenic tolerance of urinary bacteria were observed by modified Kirby-Bauer and minimum inhibitory concentration methods, respectively. The percentage of one, two, and multidrug-resistant urinary isolates were 30.4%, 37%, and 30.4%, respectively. Isolates showed variable tolerance to arsenic species. Gram-negative isolates were more tolerant to arsenic species than Gram positive. Although statistically insignificant, arsenic tolerance tended to increase from total susceptible to two-drug resistance. However, multiple drug resistance was not induced by the urinary arsenic (p>0.05). We observed moderately positive correlation between urinary arsenic level to arsenic tolerance of isolates (p<0.05). Although tolerance significantly correlated to urinary arsenic level, coselection/coresistance of arsenic to the antibiotic resistance in urinary isolates is inconclusive and remains to be further elucidated.