First record of Laem-Singh virus in black tiger shrimp (Penaeus monodon) in the Philippines

Abstract only.Laem-Singh Virus (LSNV), a single-stranded RNA virus that causes growth retardation in Penaeus monodon, is also known as Monodon Slow-Growth Syndrome (MSGS) virus. Black Tiger shrimps afflicted with this virus exhibit unusual dark color, a weight gain of less than 0.1 g in 1 to 2 weeks, unusual yellow markings, bamboo-shaped abdominal markings and brittle antennae. It was first detected in Thailand and the virus quickly spread to neighboring Asian countries such as Malaysia and Singapore. The shrimp economy of countries where infections have occurred experienced losses in the export of live shrimps and broodstocks. An earlier study in 2009 reported that LSNV was not present in the Philippines. However, since no follow-up researches were done in the succeeding years, this study was conducted to detect the presence of virus in selected sites of Luzon. Results based on biased sampling method and RT-PCR data indicated that LSNV is indeed present in the country. This is further supported by DNA sequence data, showing 100% identity with LSNV India isolate. Phylogenetic analysis showed that the Philippine isolate clustered closely with other LSNV isolates. The outcome of this study might have implications in the current practices in the Philippine shrimp aquaculture industry

Screening for in vitro systematic reviews: a comparison of screening methods and training of a machine learning classifier

Objective: Existing strategies to identify relevant studies for systematic review may not perform equally well across research domains. We compare four approaches based on either human or automated screening of either title and abstract or full text, and report the training of a machine learning algorithm to identify in vitro studies from bibliographic records. Methods: We used a systematic review of oxygen-glucose deprivation (OGD) in PC-12 cells to compare approaches. For human screening, two reviewers independently screened studies based on title and abstract or full text, with disagreements reconciled by a third. For automated screening, we applied text mining to either title and abstract or full text. We trained a machine learning algorithm with decisions from 2000 randomly selected PubMed Central records enriched with a dataset of known in vitro studies. Results: Full-text approaches performed best, with human (sensitivity: 0.990, specificity: 1.000 and precision: 0.994) outperforming text mining (sensitivity: 0.972, specificity: 0.980 and precision: 0.764). For title and abstract, text mining (sensitivity: 0.890, specificity: 0.995 and precision: 0.922) outperformed human screening (sensitivity: 0.862, specificity: 0.998 and precision: 0.975). At our target sensitivity of 95% the algorithm performed with specificity of 0.850 and precision of 0.700. Conclusion: In this in vitro systematic review, human screening based on title and abstract erroneously excluded 14% of relevant studies, perhaps because title and abstract provide an incomplete description of methods used. Our algorithm might be used as a first selection phase in in vitro systematic reviews to limit the extent of full text screening required.</p

Development and validation of methods for identification and quality assessment of in vitro research

We aim to validate machine learning methods for accurate identification of in vitro research and the subsequent assessment of risk of bias reporting of these papers. In doing so, we will address the research question: Has the reporting of risk of bias measures relevant to in vitro experiments improved over time

Application of systematic evidence mapping to identify available data on the potential human health hazards of selected market-relevant azo dyes

Background: Azo dyes are used in textiles and leather clothing. Human exposure can occur from wearing textiles containing azo dyes. Since the body’s enzymes and microbiome can cleave azo dyes, potentially resulting in mutagenic or carcinogenic metabolites, there is also an indirect health concern on the parent compounds. While several hazardous azo dyes are banned, many more are still in use that have not been evaluated systematically for potential health concerns. This systematic evidence map (SEM) aims to compile and categorize the available toxicological evidence on the potential human health risks of a set of 30 market-relevant azo dyes. Methods: Peer-reviewed and gray literature was searched and over 20,000 studies were identified. These were filtered using Sciome Workbench for Interactive computer-Facilitated Text-mining (SWIFT) Review software with evidence stream tags (human, animal, in vitro) yielding 12,800 unique records. SWIFT Active (a machine-learning software) further facilitated title/abstract screening. DistillerSR software was used for additional title/abstract, full-text screening, and data extraction. Results: 187 studies were identified that met populations, exposures, comparators, and outcomes (PECO) criteria. From this pool, 54 human, 78 animal, and 61 genotoxicity studies were extracted into a literature inventory. Toxicological evidence was abundant for three azo dyes (also used as food additives) and sparse for five of the remaining 27 compounds. Complementary search in ECHA’s REACH database for summaries of unpublished study reports revealed evidence for all 30 dyes. The question arose of how this information can be fed into an SEM process. Proper identification of prioritized dyes from various databases (including U.S. EPA’s CompTox Chemicals Dashboard) turned out to be a challenge. Evidence compiled by this SEM project can be evaluated for subsequent use in problem formulation efforts to inform potential regulatory needs and prepare for a more efficient and targeted evaluation in the future for human health assessments