RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci.

BACKGROUND: As the number of genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings in rice continues to grow, so does the already long list of genomic loci associated with important agronomic traits. Typically, loci implicated by GWAS/QTL analysis contain tens to hundreds to thousands of single-nucleotide polmorphisms (SNPs)/genes, not all of which are causal and many of which are in noncoding regions. Unraveling the biological mechanisms that tie the GWAS regions and QTLs to the trait of interest is challenging, especially since it requires collating functional genomics information about the loci from multiple, disparate data sources. RESULTS: We present RicePilaf, a web app for post-GWAS/QTL analysis, that performs a slew of novel bioinformatics analyses to cross-reference GWAS results and QTL mappings with a host of publicly available rice databases. In particular, it integrates (i) pangenomic information from high-quality genome builds of multiple rice varieties, (ii) coexpression information from genome-scale coexpression networks, (iii) ontology and pathway information, (iv) regulatory information from rice transcription factor databases, (v) epigenomic information from multiple high-throughput epigenetic experiments, and (vi) text-mining information extracted from scientific abstracts linking genes and traits. We demonstrate the utility of RicePilaf by applying it to analyze GWAS peaks of preharvest sprouting and genes underlying yield-under-drought QTLs. CONCLUSIONS: RicePilaf enables rice scientists and breeders to shed functional light on their GWAS regions and QTLs, and it provides them with a means to prioritize SNPs/genes for further experiments. The source code, a Docker image, and a demo version of RicePilaf are publicly available at https://github.com/bioinfodlsu/rice-pilaf.

Protein embeddings improve phage-host interaction prediction.

With the growing interest in using phages to combat antimicrobial resistance, computational methods for predicting phage-host interactions have been explored to help shortlist candidate phages. Most existing models consider entire proteomes and rely on manual feature engineering, which poses difficulty in selecting the most informative sequence properties to serve as input to the model. In this paper, we framed phage-host interaction prediction as a multiclass classification problem that takes as input the embeddings of a phage's receptor-binding proteins, which are known to be the key machinery for host recognition, and predicts the host genus. We explored different protein language models to automatically encode these protein sequences into dense embeddings without the need for additional alignment or structural information. We show that the use of embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features. The highest performance was obtained using the transformer-based protein language model ProtT5, resulting in a 3% to 4% increase in weighted F1 and recall scores across different prediction confidence thresholds, compared to using selected handcrafted sequence features.

Beyond Numbers: Determining the Socioeconomic and Livelihood Impacts of African Swine Fever and Its Control in the Philippines.

The impacts of African Swine Fever (ASF) have most frequently been described quantitatively though it is increasingly acknowledged these impacts extend well beyond numbers. During 2020, a multidisciplinary team of researchers developed a framework for Socioeconomic and Livelihood Impact Assessment (SELIA) of livestock diseases in smallholder communities. Two key innovations within this SELIA framework are the integration of sustainable livelihoods concepts to capture rich information beyond financial impacts, and the inclusion of stakeholders across the value chain, beyond farmers. This paper focuses on the findings from one of the first applications of the SELIA framework. In late 2020 the research team applied participatory tools from the SELIA Framework (8 focus group discussions, 14 key informant interviews, and 2 network mapping activities) to gather data to describe the impact of ASF in backyard pig-farming communities and value chains. This was undertaken across two locations in the Philippines, in turn highlighting potential leverage points for intervention. Owing to COVID-19 travel restrictions and risks, modifications to training and field activities were made. Findings from focus groups and interviews revealed the deep, emotional impacts of ASF and the associated control measures. Pigs were considered pets by many farmers and some women described them as being like their children. Animal health-workers (AHWs) also recognised the emotional toll on farmers and were sometimes strongly criticised by community members due to their involvement in depopulation campaigns. Misinformation early in the epidemic also led farmers to hide their animals from AHWs, and to dispose of them inappropriately. While the overall impact of ASF on society was negative, the impacts across different communities, scales of production and different value chain actors varied. The losses experienced by backyard farmers resulted in significant losses to linked value chain actors, such as input suppliers. This trial application of the SELIA framework revealed some complex and varied impacts of ASF. This included significant differences in livelihood and socio-economic impacts amongst different actors within value chains and also among different categories of actors (for example small, medium and large-scale traders). Repeated themes and triangulated findings suggest two leverage points for further consideration. Firstly, it is recommended a One Welfare approach to ASF control in the Philippines is explored. Emphasising careful communication between animal health-workers and farmers, and humane and sensitive pig depopulation practices. Secondly, consideration of ASF support programs tailored to sectoral and specific communities is recommended.

A Capacitive Sweat Rate Sensor for Continuous and Real-Time Monitoring of Sweat Loss.

Individualized measurement of sweat loss under heat stress is important in assessing physical performance and preventing heat-related illness for athletes or individuals working in extreme environments. The objective of this work was to develop a low-cost and easy-to-fabricate wearable sensor that enables accurate real-time measurement of sweat rate. A capacitive-type sensor was fabricated from two conducting parallel plates, plastic insulating layers, and a central microfluidic channel formed by laser cutting a plastic film. The device has no microfabricated electrodes and is assembled using adhesive tape. Sensor accuracy was validated at different flow rates and confirmed using an equivalent circuit model of the device. On-body measurements demonstrate the feasibility of real-time measurements and show good agreement with values determined from a conventional sweat collection device.

A Prospective, Multicenter Evaluation of Point-of-care Ultrasound for Small-bowel Obstruction in the Emergency Department.

OBJECTIVE: The main objective of this study was to evaluate the accuracy of emergency physician-performed point-of-care ultrasound (POCUS) for the diagnosis of small-bowel obstruction (SBO) compared to computed tomography (CT). METHODS: We performed a prospective, multicenter, observational study examining a convenience sample of adult patients with potential SBO presenting to the emergency department (ED) between July 2014 and May 2017. Each POCUS was interpreted at the bedside by the performing emergency physician and retrospectively by an expert reviewer. Test characteristics were calculated for POCUS, blinded expert interpretation, and specific POCUS parameters. RESULTS: A total of 217 subjects were included in the primary analysis with an overall SBO prevalence of 42.9%. For the diagnosis of SBO, POCUS demonstrated an overall sensitivity, specificity, positive likelihood ratio, and negative likelihood ratio of 0.88 (95% confidence interval [CI] = 0.80 to 0.94), 0.54 (95% CI = 0.45 to 0.63), 1.92 (95% CI = 1.56 to 2.35), and 0.22 (95% CI = 0.12 to 0.39), respectively. Expert review yielded a similar sensitivity (0.89 [95% CI = 0.81 to 0.95]) with a significantly higher specificity (0.82 [95% CI = 0.74 to 0.88]). The more sensitive sonographic parameters for both POC sonographers and expert reviewers were small-bowel dilation ≥ 25 mm (0.87 [95% CI = 0.79 to 0.93], 0.87 [95% CI = 0.79 to 0.93]) and abnormal peristalsis (0.82 [95% CI = 0.72 to 0.89], 0.85 [95% CI = 0.76 to 0.87]). The more specific parameters for both groups were transition point (0.82 [95% CI = 0.74 to 0.89], 0.98 [95% CI = 0.94 to 1.00]), intraperitoneal free fluid (0.82 [95% CI = 0.74 to 0.89], 0.93 [95% CI = 0.87 to 0.97]), and bowel wall edema (0.76 [95% CI = 0.67 to 0.83], 0.93 [95% CI = 0.87 to 0.97]). CONCLUSION: POCUS is moderately sensitive for SBO, although less specific, when performed by a diverse group of emergency physicians across multiple EDs. Interpretation of acquired POCUS images is significantly more accurate when performed by physicians with prior emergency ultrasound fellowship training and familiarity with the sonographic appearance of SBO.

Heterotopic ossification of the hip after non-accidental injury in a child: case report.

Heterotopic ossification is bone formation that occurs in an abnormal soft tissue location, most commonly after trauma, head injury, and surgical procedures such as joint arthroplasty. We report a rare case of severe heterotopic ossification caused by nonaccidental injury in a 3-year-old child. To our knowledge, heterotopic ossification as a result of nonaccidental injury in children has been reported in only 2 other patients. Physicians should be aware of this rare presentation of nonaccidental injury, and nonaccidental injury should be considered in the differential diagnosis in children who present with heterotopic ossification.