LABRADOR—A Computational Workflow for Virus Detection in High-Throughput Sequencing Data

High-throughput sequencing (HTS) allows detection of known and unknown viruses in samples of broad origin. This makes HTS a perfect technology to determine whether or not the biological products, such as vaccines are free from the adventitious agents, which could support or replace extensive testing using various in vitro and in vivo assays. Due to bioinformatics complexities, there is a need for standardized and reliable methods to manage HTS generated data in this field. Thus, we developed LABRADOR—an analysis pipeline for adventitious virus detection. The pipeline consists of several third-party programs and is divided into two major parts: (i) direct reads classification based on the comparison of characteristic profiles between reads and sequences deposited in the database supported with alignment of to the best matching reference sequence and (ii) de novo assembly of contigs and their classification on nucleotide and amino acid levels. To meet the requirements published in guidelines for biologicals’ safety we generated a custom nucleotide database with viral sequences. We tested our pipeline on publicly available HTS datasets and showed that LABRADOR can reliably detect viruses in mixtures of model viruses, vaccines and clinical samples.     

A novel image processing workflow for the in vivo quantification of skin microvasculature using dynamic optical coherence tomography

Background

Currently, imaging technologies that can accurately assess or provide surrogate markers of the human cutaneous microvessel network are limited. Dynamic optical coherence tomography (D‐OCT) allows the detection of blood flow in vivo and visualization of the skin microvasculature. However, image processing is necessary to correct images, filter artifacts, and exclude irrelevant signals. The objective of this study was to develop a novel image processing workflow to enhance the technical capabilities of D‐OCT.

Materials and methods

Single‐center, vehicle‐controlled study including healthy volunteers aged 18‐50 years. A capsaicin solution was applied topically on the subject's forearm to induce local inflammation. Measurements of capsaicin‐induced increase in dermal blood flow, within the region of interest, were performed by laser Doppler imaging (LDI) (reference method) and D‐OCT.

Results

Sixteen subjects were enrolled. A good correlation was shown between D‐OCT and LDI, using the image processing workflow. Therefore, D‐OCT offers an easy‐to‐use alternative to LDI, with good repeatability, new robust morphological features (dermal‐epidermal junction localization), and quantification of the distribution of vessel size and changes in this distribution induced by capsaicin. The visualization of the vessel network was improved through bloc filtering and artifact removal. Moreover, the assessment of vessel size distribution allows a fine analysis of the vascular patterns.

Conclusion

The newly developed image processing workflow enhances the technical capabilities of D‐OCT for the accurate detection and characterization of microcirculation in the skin. A direct clinical application of this image processing workflow is the quantification of the effect of topical treatment on skin vascularization.

     

优化溶栓流程对轻型急性缺血性卒中院内延误及预后的影响

目的分析优化溶栓流程对轻型急性缺血性卒中患者院内延误及预后的影响。方法回顾性收集秦皇岛市第一医院2015年7月-2017年6月行静脉溶栓治疗的轻型缺血性卒中患者资料。按照流程优化时间前后,分为优化组和对照组。比较两组入院到溶栓时间(door to needle time,DNT)、溶栓后7 d NIHSS评分和溶栓后3个月mRS评分。结果共纳入57例轻型缺血性卒中患者,平均年龄61.7±5.4岁,男性44例(77.2%)。其中对照组24例,优化组33例。两组患者一般资料比较差异无统计学意义。与对照组比较,优化组DNT缩短(68.7±19.1 vs 88.8±23.1 min,P=0.001),DNT≤60 min的患者比例更高(42.4%vs 12.5%,P=0.015);溶栓治疗后3个月mRS评分更低[0(0～0.5)vs 0.5(0～2),P=0.017],良好预后(mRS评分≤1分)患者比例更高(87.9%vs 62.5%,P=0.024)。结论优化溶栓流程可以缩短轻型急性缺血性卒中患者的DNT,提高DNT≤60 min达标率,改善患者3个月预后。     

Collaborative co-design of emerging multi-technologies for surgery

The EU Research Training Network on Augmented Reality in Surgery (ARIS*ER) was established with two aims: (1) to develop next-generation novel image guidance (augmented reality based on medical images) and cross-linked robotic systems (automatic control loops guided by information sensed from the patient) and (2) to educate young researchers in the user-centred, multidisciplinary design of emerging technologies for minimally invasive surgery (MIS) and intervention radiology. Collaborations between engineers, Human Factors specialists, industrial designers and medical end users were foreseen, but actual methodologies had to be developed. Three applications were used as development vehicles and as demonstrators. The resulting teamwork and process of identifying requirements, finding solutions (in technology and workflow), and shifting between these to optimize and speed development towards quality of care were studied. The ARIS*ER approach solves current problems in collaborative teams, taking a systems approach, and manages the overview of requirements and solutions, which is too complex to manage centrally.     

Development of an advanced database for clinical trials integrated with an electronic patient record system

Secondary use of patient databases is essential in healthcare if clinical trials are to progress efficiently to planned time and target and imperative if the planned UK expansion of research and development (R&D) at point of care is to be achieved. Integration of effective databases primarily designed to facilitate patient care with R&D requirements is needed but represents a complex challenge.We present a system that achieves an integrated approach with online management of complex datasets for clinical trials within care records using a specific study as an example to show functionality in practice; illustrating how this system provides an ideal resource to meet the needs of both clinicians and researchers.     

企业级医疗影像信息集成平台研究

目的:探讨大型医院内部各影像系统信息共享和医疗资源整合方法.方法:采用IHE技术框架为理论指导,结合国内医院实际提出"企业级医疗影像信息集成平台"及其开放整合方案,通过各厂商的密切配合、实施,初步实现对全院DICOM影像的统一归档和统一发布.结果:经过实践验证,集成平台切实有效,既提高临床医生对医学影像信息的使用效率,提高诊疗质量,又便于医信技术人员对影像信息的集成管理.结论:基于IHE技术框架的企业级影像信息集成平台研究被证明是可行、可靠和有效的.