Project description:The knowledge-action gap in conservation science and practice occurs when research outputs do not result in actions to protect or restore biodiversity. Among the diverse and complex reasons for this gap, three barriers are fundamental: knowledge is often unavailable to practitioners and challenging to interpret or difficult to use or both. Problems of availability, interpretability, and useability are solvable with open science practices. We considered the benefits and challenges of three open science practices for use by conservation scientists and practitioners. First, open access publishing makes the scientific literature available to all. Second, open materials (detailed methods, data, code, and software) increase the transparency and use of research findings. Third, open education resources allow conservation scientists and practitioners to acquire the skills needed to use research outputs. The long-term adoption of open science practices would help researchers and practitioners achieve conservation goals more quickly and efficiently and reduce inequities in information sharing. However, short-term costs for individual researchers (insufficient institutional incentives to engage in open science and knowledge mobilization) remain a challenge. We caution against a passive approach to sharing that simply involves making information available. We advocate a proactive stance toward transparency, communication, collaboration, and capacity building that involves seeking out and engaging with potential users to maximize the environmental and societal impact of conservation science.
Project description:Despite early predictions and rapid progress in research, the introduction of personal genomics into clinical practice has been slow. Several factors contribute to this translational gap between knowledge and clinical application. The evidence available to support genetic test use is often limited, and implementation of new testing programs can be challenging. In addition, the heterogeneity of genomic risk information points to the need for strategies to select and deliver the information most appropriate for particular clinical needs. Accomplishing these tasks also requires recognition that some expectations for personal genomics are unrealistic, notably expectations concerning the clinical utility of genomic risk assessment for common complex diseases. Efforts are needed to improve the body of evidence addressing clinical outcomes for genomics, apply implementation science to personal genomics, and develop realistic goals for genomic risk assessment. In addition, translational research should emphasize the broader benefits of genomic knowledge, including applications of genomic research that provide clinical benefit outside the context of personal genomic risk.
Project description:The article presents an AI-based fungi species recognition system for a citizen-science community. The system's real-time identification too - FungiVision - with a mobile application front-end, led to increased public interest in fungi, quadrupling the number of citizens collecting data. FungiVision, deployed with a human-in-the-loop, reaches nearly 93% accuracy. Using the collected data, we developed a novel fine-grained classification dataset - Danish Fungi 2020 (DF20) - with several unique characteristics: species-level labels, a small number of errors, and rich observation metadata. The dataset enables the testing of the ability to improve classification using metadata, e.g., time, location, habitat and substrate, facilitates classifier calibration testing and finally allows the study of the impact of the device settings on the classification performance. The continual flow of labelled data supports improvements of the online recognition system. Finally, we present a novel method for the fungi recognition service, based on a Vision Transformer architecture. Trained on DF20 and exploiting available metadata, it achieves a recognition error that is 46.75% lower than the current system. By providing a stream of labeled data in one direction, and an accuracy increase in the other, the collaboration creates a virtuous cycle helping both communities.
Project description:Despite continuous updates of the human reference genome, there are still hundreds of unresolved gaps which account for about 5% of the total sequence length. Given the availability of whole genome de novo assemblies, especially those derived from long-read sequencing data, gap-closing sequences can be determined. By comparing 17 de novo long-read sequencing assemblies with the human reference genome, we identified a total of 1,125 gap-closing sequences for 132 (16.9% of 783) gaps and added up to 2.2 Mb novel sequences to the human reference genome. More than 90% of the non-redundant sequences could be verified by unmapped reads from the Simons Genome Diversity Project dataset. In addition, 15.6% of the non-reference sequences were found in at least one of four non-human primate genomes. We further demonstrated that the non-redundant sequences had high content of simple repeats and satellite sequences. Moreover, 43 (32.6%) of the 132 closed gaps were shown to be polymorphic; such sequences may play an important biological role and can be useful in the investigation of human genetic diversity.
Project description:BACKGROUND:The fast reduction of prices of DNA sequencing allowed rapid accumulation of genome data. However, the process of obtaining complete genome sequences is still very time consuming and labor demanding. In addition, data produced from various sequencing technologies or alternative assemblies remain underexplored to improve assembly of incomplete genome sequences. FINDINGS:We have developed FGAP, a tool for closing gaps of draft genome sequences that takes advantage of different datasets. FGAP uses BLAST to align multiple contigs against a draft genome assembly aiming to find sequences that overlap gaps. The algorithm selects the best sequence to fill and eliminate the gap. CONCLUSIONS:FGAP reduced the number of gaps by 78% in an E. coli draft genome assembly using two different sequencing technologies, Illumina and 454. Using PacBio long reads, 98% of gaps were solved. In human chromosome 14 assemblies, FGAP reduced the number of gaps by 35%. All the inserted sequences were validated with a reference genome using QUAST. The source code and a web tool are available at http://www.bioinfo.ufpr.br/fgap/.
Project description:Topological phase transition is accompanied with a change of topological numbers. According to the bulk-edge correspondence, the gap closing and the breakdown of the adiabaticity are necessary at the phase transition point to make the topological number ill-defined. However, the gap closing is not always needed. In this paper, we show that two topological distinct phases can be continuously connected without gap closing, provided the symmetry of the system changes during the process. Here we propose the generic principles how this is possible by demonstrating various examples such as 1D polyacetylene with the charge-density-wave order, 2D silicene with the antiferromagnetic order, 2D silicene or quantum well made of HgTe with superconducting proximity effects and 3D superconductor Cu doped Bi2Se3. It is argued that such an unusual phenomenon can occur when we detour around the gap closing point provided the connection of the topological numbers is lost along the detour path.
Project description:Type 2 diabetes mellitus (T2DM) is associated with marked cardiovascular (CV) morbidity and mortality, including heart failure (HF). Until recently, an oral glucose-lowering agent that improved hyperglycemia as well as provided CV benefits in patients with T2DM and cardiovascular disease (CVD) was lacking. The newest class of glucose-lowering agents, sodium glucose cotransporter 2 (SGLT2) inhibitors, includes canagliflozin, dapagliflozin, and empagliflozin. Prior to the release of the LEADER trial results, the recent EMPA-REG OUTCOME study was the only dedicated CV trial to demonstrate a reduction in major adverse cardiac events, CV mortality, and all-cause mortality and a reduction in hospitalization for HF with empagliflozin, given on top of standard-of-care therapy in patients with T2DM and CVD. This paper summarizes the results from EMPA-REG OUTCOME and discusses their significance and clinical implications.
Project description:Clinical audit of invasive mold disease (IMD) in hematology patients is inefficient due to the difficulties of case finding. This results in antifungal stewardship (AFS) programs preferentially reporting drug cost and consumption rather than measures that actually reflect quality of care. We used machine learning-based natural language processing (NLP) to non-selectively screen chest tomography (CT) reports for pulmonary IMD, verified by clinical review against international definitions and benchmarked against key AFS measures. NLP screened 3014 reports from 1 September 2008 to 31 December 2017, generating 784 positives that after review, identified 205 IMD episodes (44% probable-proven) in 185 patients from 50,303 admissions. Breakthrough-probable/proven-IMD on antifungal prophylaxis accounted for 60% of episodes with serum monitoring of voriconazole or posaconazole in the 2 weeks prior performed in only 53% and 69% of episodes, respectively. Fiberoptic bronchoscopy within 2 days of CT scan occurred in only 54% of episodes. The average turnaround of send-away bronchoalveolar galactomannan of 12 days (range 7-22) was associated with high empiric liposomal amphotericin consumption. A random audit of 10% negative reports revealed two clinically significant misses (0.9%, 2/223). This is the first successful use of applied machine learning for institutional IMD surveillance across an entire hematology population describing process and outcome measures relevant to AFS. Compared to current methods of clinical audit, semi-automated surveillance using NLP is more efficient and inclusive by avoiding restrictions based on any underlying hematologic condition, and has the added advantage of being potentially scalable.
Project description:Single-unit responses and population codes differ in the "read-out" information they provide about high-level visual representations. Diverging local and global read-outs can be difficult to reconcile with in vivo methods. To bridge this gap, we studied the relationship between single-unit and ensemble codes for identity, gender, and viewpoint, using a deep convolutional neural network (DCNN) trained for face recognition. Analogous to the primate visual system, DCNNs develop representations that generalize over image variation, while retaining subject (e.g., gender) and image (e.g., viewpoint) information. At the unit level, we measured the number of single units needed to predict attributes (identity, gender, viewpoint) and the predictive value of individual units for each attribute. Identification was remarkably accurate using random samples of only 3% of the network's output units, and all units had substantial identity-predicting power. Cross-unit responses were minimally correlated, indicating that single units code non-redundant identity cues. Gender and viewpoint classification required large-scale pooling of units-individual units had weak predictive power. At the ensemble level, principal component analysis of face representations showed that identity, gender, and viewpoint separated into high-dimensional subspaces, ordered by explained variance. Unit-based directions in the representational space were compared with the directions associated with the attributes. Identity, gender, and viewpoint contributed to all individual unit responses, undercutting a neural tuning analogy. Instead, single-unit responses carry superimposed, distributed codes for face identity, gender, and viewpoint. This undermines confidence in the interpretation of neural representations from unit response profiles for both DCNNs and, by analogy, high-level vision.
Project description:Men have been observed to have a greater willingness to compete compared to women, and it is possible that this contributes to gender differences in wages and career advancement. Policy interventions such as quotas are sometimes used to remedy this but these may cause unintended side-effects. Here, we present experimental evidence that a simple and practically costless tool-priming subjects with power-can close the gender gap in competitiveness. While in a neutral as well as in a low-power priming situation men are much more likely than women to choose competition, this gap vanishes when subjects are primed with a high-power situation. We show that priming with high power makes competition entry decisions more realistic and also that it reduces the level of risk tolerance among male participants, which can help explain why it leads to a closing down of the gender gap in competitiveness.