Demonstration-based learning for few-shot biomedical named entity recognition under machine reading comprehension

Although deep learning techniques have shown significant achievements, they frequently depend on extensive amounts of hand-labeled data and tend to perform inadequately in few-shot scenarios. The objective of this study is to devise a strategy that can improve the model's capability to recognize biomedical entities in scenarios of few-shot learning. By redefining biomedical named entity recognition (BioNER) as a machine reading comprehension (MRC) problem, we propose a demonstration-based learning method to address few-shot BioNER, which involves constructing appropriate task demonstrations. In assessing our proposed method, we compared the proposed method with existing advanced methods using six benchmark datasets, including BC4CHEMD, BC5CDR-Chemical, BC5CDR-Disease, NCBI-Disease, BC2GM, and JNLPBA. We examined the models' efficacy by reporting F1 scores from both the 25-shot and 50-shot learning experiments. In 25-shot learning, we observed 1.1% improvements in the average F1 scores compared to the baseline method, reaching 61.7%, 84.1%, 69.1%, 70.1%, 50.6%, and 59.9% on six datasets, respectively. In 50-shot learning, we further improved the average F1 scores by 1.0% compared to the baseline method, reaching 73.1%, 86.8%, 76.1%, 75.6%, 61.7%, and 65.4%, respectively. We reported that in the realm of few-shot learning BioNER, MRC-based language models are much more proficient in recognizing biomedical entities compared to the sequence labeling approach. Furthermore, our MRC-language models can compete successfully with fully-supervised learning methodologies that rely heavily on the availability of abundant annotated data. These results highlight possible pathways for future advancements in few-shot BioNER methodologies

Ketogenic Diet as a Treatment for Super-Refractory Status Epilepticus in Febrile Infection-Related Epilepsy Syndrome

Background: Febrile infection-related epilepsy syndrome (FIRES) is a fatal epileptic encephalopathy associated with super-refractory status epilepticus (SRSE). Several treatment strategies have been proposed for this condition although the clinical outcomes are poor. Huge efforts from neurointensivists have been focused on identifying the characteristics of FIRES and treatment to reduce the mortality associated with this condition. However, the role of ketogenic diet (KD) in FIRES is not fully understood.Methods: We performed a retrospective review of patients who met the diagnostic criteria of FIRES, SRSE, and were treated with KD between 2015 and 2018 at the Department of Pediatrics, Xiangya Hospital of Central South University. The following data were recorded: demographic features, clinical presentation, anticonvulsant treatment, timing and duration of KD and follow-up information. Electroencephalography recordings were reviewed and analyzed.Results: Seven patients with FIRES were put on KD (5 via enteral route, and 2 via intravenous line) for SRSE in the PICU. The median age was 8. Four patients were male and 3 were female. Although patients underwent treatment with a median of 4 antiepileptic drugs and 2 anesthetic agents, the status epilepticus (SE) persisted for 7–31 days before KD initiation. After KD initiation, all patients achieved ketosis and SE disappeared within an average of 5 days (IQR 3.5), although there were minor side effects. In 6 patients, a unique pattern was identified in the EEG recording at the peak period. After initiation of KD, the number of seizures reduced, the duration of seizure shortened, the background recovered and sleep architecture normalized in the EEG recordings. The early initiation of KD (at the onset of SE) in the acute phase of patients decreased the mRS score in the subsequent period (p = 0.012, r = 0.866).Conclusions: The characteristic EEG pattern in the acute phase promoted timely diagnosis of FIRES. Our data suggest that KD may be a safe and promising therapy for FIRES with SRSE, and that early initiation of KD produces a favorable prognosis. Therefore, KD should be applied earlier in the course of FIRES. Intravenous KD can be an effective alternative route of administration for patients who may not take KD enterally

Thoracic endovascular aortic repair under venoarterial extracorporeal membrane oxygenation for acute aortic dissection patients: a case report

BackgroundOpen repair and replacement of the diseased aorta is still the standard treatment for type A aortic dissection (TAAD) in most patients. In endovascular treatment alone, ensuring adequate blood supply to the brain while covering the dissection with a stent is difficult.Case presentationThis study includes a 71-year-old male patient with type A aortic dissection presented at a recent follow-up examination after having undergone thoracic endovascular aortic repair (TEVAR) plus left subclavian artery chimney stent reconstruction for descending aortic dissection 5 years ago. Preoperative computed tomographic angiography, computed tomographic perfusion, and transcranial Doppler showed an intact cerebral arterial ring and good collateral circulation. We successfully performed an endovascular repair of the thoracic aorta with venoarterial extracorporeal membrane oxygenation (V-A ECMO) to protect the craniocerebral blood supply, greatly increase the safety of the operation, and ensure a good prognosis.ConclusionTEVAR under V-A ECMO protection is beneficial for patients with TAAD because of its minimal trauma, rapid recovery, few complications, and low mortality

Knowledge, attitudes and practices (KAP) relating to avian influenza in urban and rural areas of China

<p>Abstract</p> <p>Background</p> <p>Studies have revealed that visiting poultry markets and direct contact with sick or dead poultry are significant risk factors for H5N1 infection, the practices of which could possibly be influenced by people's knowledge, attitudes and practices (KAPs) associated with avian influenza (AI). To determine the KAPs associated with AI among the Chinese general population, a cross-sectional survey was conducted in China.</p> <p>Methods</p> <p>We used standardized, structured questionnaires distributed in both an urban area (Shenzhen, Guangdong Province; n = 1,826) and a rural area (Xiuning, Anhui Province; n = 2,572) using the probability proportional to size (PPS) sampling technique.</p> <p>Results</p> <p>Approximately three-quarters of participants in both groups requested more information about AI. The preferred source of information for both groups was television. Almost three-quarters of all participants were aware of AI as an infectious disease; the urban group was more aware that it could be transmitted through poultry, that it could be prevented, and was more familiar with the relationship between AI and human infection. The villagers in Xiuning were more concerned than Shenzhen residents about human AI viral infection. Regarding preventative measures, a higher percentage of the urban group used soap for hand washing whereas the rural group preferred water only. Almost half of the participants in both groups had continued to eat poultry after being informed about the disease.</p> <p>Conclusions</p> <p>Our study shows a high degree of awareness of human AI in both urban and rural populations, and could provide scientific support to assist the Chinese government in developing strategies and health-education campaigns to prevent AI infection among the general population.</p

Genomes shed light on the evolution of Begonia, a mega‐diverse genus

Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with ~2,000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana, and B. peltatifolia), and whole genome shot-gun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22,059 - 23,444 protein-coding genes. Synteny analysis revealed a lineage specific whole-genome duplication (WGD) that occurred just before the diversification of the Begonia. Functional enrichment of gene families retained after WGD highlight the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade-adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade

Biomedical applications of adaptive optical interferometry

Adaptive interferometry uses a self-adaptive beam mixer instead of a passive beam mixer as conventional interferometry does. A photorefractive quantum well device acting as an adaptive beam mixer in a two-wave mixing geometry stabilizes the interferometric phase in the far field. Advantages of adaptive interferometry are explored in two kinds of biomedicine: adaptive optical coherence reflectometry for biomedical imaging and adaptive optical bio-compact (BioCD) disk for biosensing. Adaptive Optical Coherent Domain Reflectometry (OCDR) used adaptive ultrafast pulse mixing as the coherent gate for OCDR for the first time. Studied homodyne signals from the adaptive pulse-mixing effect, as well as the sensitivity and noise by both experiments and simulations. Demonstrated the addition ability of laser based ultrasound detection of this technique. Adaptive BioCD is an adaptive interferometric technique for biomolecule sensing and fast surface topography with atomic microscope grade accuracy. The technique directly detects the optical thickness of biomolecule patterns immobilized on a flat surface. The surface is scanned in a spinning-disk design, like reading a CD, which provides fast readout and huge surface area for space-divided multi-analyte immunoassay detection by measuring the optical thickness change due to local reactions. Immunoassay experiments successfully detected binding between antibodies and immobilized antigens in a 2-analyte immunoassay with high specificity and without observable cross-reactivity. The system achieved sensitivity in optical thickness of less than one tenth of a monolayer of protein

Cellular resolution multiplexed FLIM tomography with dual-color Bessel beam

Fourier multiplexed FLIM (FmFLIM) tomography enables multiplexed 3D lifetime imaging of whole embryos. In our previous FmFLIM system, the spatial resolution was limited to 25 mu m because of the trade-off between the spatial resolution and the imaging depth. In order to achieve cellular resolution imaging of thick specimens, we built a tomography system with dual-color Bessel beam. In combination with FmFLIM, the Bessel FmFLIM tomography system can perform parallel 3D lifetime imaging on multiple excitation-emission channels at a cellular resolution of 2.8 mu m. The image capability of the Bessel FmFLIM tomography system was demonstrated by 3D lifetime imaging of dual-labeled transgenic zebrafish embryos. (C) 2017 Optical Society of AmericaNational Institutes of Health (NIH) [R00EB008737, R01EB015481]; NIH [R00DK091405]; American Society of Nephrology; National Kidney FoundationOpen Access Journal.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]