Case-control Indian buffet process identifies biomarkers of response to Codrituzumab

SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts

MOTIVATION

Multi-strain infection is a common yet under-investigated phenomenon of many pathogens. Currently, biologists analyzing SNP information sometimes have to discard mixed infection samples as many downstream analyses require monogenomic inputs. Such a protocol impedes our understanding of the underlying genetic diversity, co-infection patterns, and genomic relatedness of pathogens. A scalable tool to learn and resolve the SNP-haplotypes from polygenomic data is an urgent need in molecular epidemiology.

RESULTS

We develop a slice sampling Markov Chain Monte Carlo algorithm, named SNP-Slice, to learn not only the SNP-haplotypes of all strains in the populations but also which strains infect which hosts. Our method reconstructs SNP-haplotypes and individual heterozygosities accurately without reference panels and outperforms the state-of-the-art methods at estimating the multiplicity of infections and allele frequencies. Thus, SNP-Slice introduces a novel approach to address polygenomic data and opens a new avenue for resolving complex infection patterns in molecular surveillance. We illustrate the performance of SNP-Slice on empirical malaria and HIV datasets and provide recommendations for using our method on empirical datasets.

AVAILABILITY AND IMPLEMENTATION

The implementation of the SNP-Slice algorithm, as well as scripts to analyze SNP-Slice outputs, are available at https://github.com/nianqiaoju/snp-slice.

Distinct neurocognitive fingerprints reflect differential associations with risky and impulsive behavior in a neurotypical sample

Engagement in risky and impulsive behavior has long been associated with deficits in neurocognition. However, we have a limited understanding of how multiple subfunctions of neurocognition co-occur within individuals and which combinations of neurocognitive subfunctions are most relevant for risky and impulsive behavior. Using the neurotypical Nathan Kline Institute Rockland Sample (N = 673), we applied a Bayesian latent feature learning model-the Indian Buffet Process-to identify nuanced, individual-specific profiles of multiple neurocognitive subfunctions and examine their relationship to risky and impulsive behavior. All features were within a relatively normative range of neurocognition; however, there was subtle variability related to risky and impulsive behaviors. The relatively overall poorer neurocognition feature correlated with greater affective impulsivity and substance use patterns/problems. The poorer episodic memory and emotion feature correlated with greater trait externalizing and sensation-seeking. The poorer attention feature correlated with increased trait externalizing and negative urgency but decreased positive urgency and substance use. Finally, the average or mixed features negatively correlated with various risky and impulsive behaviors. Estimating nuanced patterns of co-occurring neurocognitive functions can inform our understanding of a continuum of risky and impulsive behaviors.

Advances in the conventional clinical treatment for hepatoblastoma and therapeutic innovation

Background

Hepatoblastoma (HB) is a rare malignancy usually occurring in children under 3 years old. With advancements in surgical techniques and molecular biology, new treatments have been developed.

Data resources

The recent literatures on new treatments, molecular mechanisms and clinical trials for HB were searched and reviewed.

Results

Surgical resection remains the main option for treatment of HB. Although complete resection is recommended, a resection with microscopical positive margins (R1) may have similar 5-year overall survival and 5-year event-free survival (EFS) rates after cisplatin chemotherapy and the control of metastasis, as only once described so far. Indocyanine green-guided surgery can help achieve precise resection. Additionally, associating liver partition and portal vein ligation for staged hepatectomy can rapidly increase future liver remnant volume compared with portal vein ligation or embolization. Cisplatin-containing chemotherapies slightly differ among the guidelines from the International Childhood Liver Tumors Strategy Group (SIOPEL), Children’s Oncology Group (COG) and Chinese Anti-Cancer Association Pediatric Committee (CCCG), and the 3-year EFS rate of patients in SIOPEL and CCCG studies was recently shown to be higher than that in COG studies. Liver transplantation is an option for patients with unresectable HB, and successful cases of autologous liver transplantation have been reported. In addition, effective inhibitors of important targets, such as the mTOR (mammalian target of rapamycin) inhibitor rapamycin, β-catenin inhibitor celecoxib and EpCAM (epithelial cell adhesion molecule) inhibitor catumaxomab, have been demonstrated to reduce the activity of HB cells and to control metastasis in experimental research and clinical trials.

Conclusion

These advances in surgical and medical treatment provide better outcomes for children with HB, and identifying novel targets may lead to the development of future targeted therapies and immunotherapies.