Use of Machine Learning and Artificial Intelligence to predict SARS-CoV-2 infection from Full Blood Counts in a population

Since December 2019 the novel coronavirus SARS-CoV-2 has been identified as the cause of the pandemic COVID-19. Early symptoms overlap with other common conditions such as common cold and Influenza, making early screening and diagnosis are crucial goals for health practitioners. The aim of the study was to use machine learning (ML), an artificial neural network (ANN) and a simple statistical test to identify SARS-CoV-2 positive patients from full blood counts without knowledge of symptoms or history of the individuals. The dataset included in the analysis and training contains anonymized full blood counts results from patients seen at the Hospital Israelita Albert Einstein, at São Paulo, Brazil, and who had samples collected to perform the SARS-CoV-2 rt-PCR test during a visit to the hospital. Patient data was anonymised by the hospital, clinical data was standardized to have a mean of zero and a unit standard deviation. This data was made public with the aim to allow researchers to develop ways to enable the hospital to rapidly predict and potentially identify SARS-CoV-2 positive patients.We find that with full blood counts random forest, shallow learning and a flexible ANN model predict SARS-CoV-2 patients with high accuracy between populations on regular wards (AUC = 94–95%) and those not admitted to hospital or in the community (AUC = 80–86%). Here, AUC is the Area Under the receiver operating characteristics Curve and a measure for model performance. Moreover, a simple linear combination of 4 blood counts can be used to have an AUC of 85% for patients within the community. The normalised data of different blood parameters from SARS-CoV-2 positive patients exhibit a decrease in platelets, leukocytes, eosinophils, basophils and lymphocytes, and an increase in monocytes.SARS-CoV-2 positive patients exhibit a characteristic immune response profile pattern and changes in different parameters measured in the full blood count that are detected from simple and rapid blood tests. While symptoms at an early stage of infection are known to overlap with other common conditions, parameters of the full blood counts can be analysed to distinguish the viral type at an earlier stage than current rt-PCR tests for SARS-CoV-2 allow at present. This new methodology has potential to greatly improve initial screening for patients where PCR based diagnostic tools are limited.     

功能性消化不良患者的外周血白细胞分析

背景　功能性消化不良（FD）是我国消化系统的常见病、多发病,既往研究较少关注患者的临床检验指标。目的　观察FD患者外周血白细胞情况,并分析其与健康者之间的差异。方法　选取2016-2018年就诊于中日友好医院脾胃病科门诊且确诊为FD的患者为FD组（n=87）,选取同期于本院工作的健康职工及行体检的健康志愿者为对照组（n=45）。收集两组外周血白细胞计数、中性粒细胞计数、中性粒细胞分数、嗜酸粒细胞计数情况,进行异常率和具体数值的比较;并对两组不同性别的人群进行白细胞分析。结果　FD组女性所占比例高于对照组（P<0.05）。FD组白细胞计数异常者15例,均表现为偏低;对照组白细胞总数异常者1例,也表现为偏低。FD组中性粒细胞计数异常者16例,均表现为偏低;对照组中性粒细胞计数异常者1例,也表现为偏低。FD组中性粒细胞分数异常者4例,其中1例表现为偏低,3例表现为偏高;对照组中性粒细胞分数异常者3例,其中2例表现为偏低,1例表现为偏高。FD组嗜酸粒细胞计数异常者2例,均表现为偏高;健康组嗜酸粒细胞计数异常者1例,表现为偏高。FD组白细胞计数、中性粒细胞计数异常率高于对照组（P<0.05）。FD组白细胞计数、中性粒细胞计数低于对照组（P<0.05）。女性FD患者白细胞计数、中性粒细胞计数低于健康女性（P<0.05）。结论　FD患者白细胞计数及中性粒细胞计数较健康人群偏低,白细胞计数、中性粒细胞计数异常率较健康人群高,且这种现象在女性FD患者中更突出。     

Acute sleep deprivation in healthy young men: Impact on population diversity and function of circulating neutrophils

Lack of sleep greatly affects our immune system. The present study investigates the acute effects of total sleep deprivation on blood neutrophils, the most abundant immune cell in our circulation and the first cell type recruited to sites of infection. Thus, the population diversity and function of circulating neutrophils were compared in healthy young men following one night of total sleep deprivation (TSD) or after 8 h regular sleep. We found that neutrophil counts were elevated after nocturnal wakefulness (2.0 ± 0.2 × 10⁹/l vs. 2.6 ± 0.2 × 10⁹/l, sleep vs. TSD, respectively) and the population contained more immature CD16^dim/CD62L^bright cells (0.11 ± 0.040 × 10⁹/l [5.5 ± 1.1%] vs. 0.26 ± 0.020 × 10⁹/l [9.9 ± 1.4%]). As the rise in numbers of circulating mature CD16^bright/CD62L^bright neutrophils was less pronounced, the fraction of this subpopulation showed a significant decrease (1.8 ± 0.15 × 10⁹/l [88 ± 1.8%] vs. 2.1 ± 0.12 × 10⁹/l [82 ± 2.8%]). The surface expression of receptors regulating mobilization of neutrophils from bone marrow was decreased (CXCR4 and CD49d on immature neutrophils; CXCR2 on mature neutrophils). The receptor CXCR2 is also involved in the production of reactive oxygen species (ROS), and in line with this, total neutrophils produced less ROS. In addition, following sleep loss, circulating neutrophils exhibited enhanced surface levels of CD11b, which indicates enhanced granular fusion and concomitant protein translocation to the membrane. Our findings demonstrate that sleep loss exerts significant effects on population diversity and function of circulating neutrophils in healthy men. To which extent these changes could explain as to why people with poor sleep patterns are more susceptible to infections warrants further investigation.     

实时荧光定量端粒重复扩增法检测大肠癌患者单个核细胞端粒酶基因表达

目的 研究大肠癌患者外周血单个核细胞(PBMC)端粒酶基因表达与临床病理的关系.方法 用实时荧光定量端粒重复扩增法(RTQ-TRAP)检测71例大肠癌和20例良性大肠疾病患者,以及25名健康人PBMC端粒酶基因表达,同时检测大肠癌患者血浆癌胚抗原(CEA)含量.结果 71例大肠癌患者中,50例端粒酶基因表达阳性,阳性率70.4%;20例良性大肠疾病表达阳性1例,阳性率为5.0%,大肠癌组与良性大肠疾病组和健康对照组的PBMC端粒酶基因表达差异有统计学意义(χ2=24.521,P<0.001).大肠癌患者在不同性别(χ2=0.114,P=0.736)、年龄(χ2=0.113,P=0.735)、肿瘤部位(χ2=1.523,P=0.677)、Dukes分期(χ2=2.282,P=0.320)间的端粒酶基因表达差异无统计学意义.71例大肠癌患者PBMC端粒酶基因表达阳性率与CEA阳性率(63.4%)比较,差异无统计学意义(χ2=2.286,P=0.125).结论 RTQ-TRAP是一种快速、准确、定量检测端粒酶基因表达的方法,大肠癌患者PBMC端粒酶活性是一项有效的辅助诊断大肠癌的分子标志.     

Acromioclavicular joint septic arthritis in an immunocompetent child: A case report

Septic arthritis of acromioclavicular (AC) joint is a rare entity. It is generally seen in patients who are immunocompromised. Only 15 cases have been reported till now, with only one case series of 6 patients. We report a case of septic arthritis of AC joint in an immunocompetent child. A 9 years old girl presented with history of pain in left shoulder for 4 days associated with fever. No history suggestive of any immunocompromised state was complained. On local examination, a swelling of around 3 cm in diameter was found over left AC joint region with raised local temperature, tenderness on palpation and positive response in fluctuation test. Total leukocyte count was 18.7 × 10⁹/L with 80% of neutrophils. Erythrocyte sedimentation rate (ESR) was 28 mm/1 h. C-reactive protein (CRP) was 12 mg/L. X-ray showed enlarged left AC joint space. Ultrasound revealed hypoechoic collection in the AC joint and the surrounding area. The aspirate was thick and purulent in nature, revealing Gram positive cocci at staining. Arthrotomy and thorough lavage of AC joint was done. Culture of the aspirate showed Methicillin Resistant Staphylococcus Aureus (MRSA) after 48 hours that was sensitive to amikacin, gentamicin, erythromycin and teicoplanin. Patient was symptom-free at 2 months of follow-up with no signs of osteomyelitis on the radiographs. Thus this is the first case of AC joint septic arthritis in healthy individual. Being proximal to the shoulder joint, AC joint septic arthritis can be confused with the shoulder joint septic arthritis. Thus, high index of suspicion is required for accurate diagnosis.     

Atraumatic Pulsatile Leukocyte Circulation for Long‐Term In Vitro Dynamic Culture and Adhesion Assays

Low flow rate pumping of cell suspensions finds current applications in bioreactors for short‐term dynamic cell culture and adhesion assays. The aim of this study was to develop an atraumatic pump and hemodynamically adapted test circuit to allow operating periods of at least several hours. A computer‐controlled mini‐pump (MP) was constructed based on non‐occlusive local compression of an elastic tube with commercial bi‐leaflet valves directing the pulsatile flow into a compliant circuit. Cell damage and activation in the system were tested with whole blood in comparison with a set with a conventional peristaltic pump (PP). Activation of circulating THP‐1 monocytes was tested by measuring the expression of CD54 (ICAM‐1). Additionally, monocyte‐endothelial interactions were monitored using a parallel‐plate flow chamber with an artificial stenosis. The system required a priming volume of only 20 mL, delivering a peak pulsatile flow of up to 35 mL/min. After 8 h, blood hemolysis was significantly lower for MP with 11 ± 3 mg/dL compared with PP with 100 ± 16 mg/dL. CD142 (tissue factor) expression on blood monocytes was 50% lower for MP. With MP, THP‐1 cells could be pumped for extended periods (17 h), with no enhanced expression of CD54 permitting the long‐term co‐culture of THP‐1 with endothelial cells and the analysis of flow pattern effects on cell adhesion. A low‐damage assay setup was developed, which allows the pulsatile flow of THP‐1 cells and investigation of their interaction with other cells or surfaces for extended periods of time.     

原发性胆汁性肝硬化患者外周血单个核细胞中趋化因子受体CXCR3 mRNA表达水平变化

目的 探讨原发性胆汁性肝硬化(PBC)患者外周血单个核细胞(PBMC)中CXCR3mRNA表达及其与疾病发病机制、疾病活动性的关系.方法 采用逆转录实时荧光定量(FQ-RT)-PCR的方法,在Light Cycler Real time PCR检测仪上检测59例PBC患者(活动期29例、缓解期30例)、结缔组织病(CTD)患者20例(疾病对照组)、健康体检者29名(健康对照组)外周血PBMC中CXCR3 mRNA的表达水平和含量.以Act=Ct(待测基因)-Ct(内参基因)比较基因表达水平的变化.结果 活动期PBC患者CXCR3 mRNA表达水平(Act=5.41±2.69)明显高于缓解期PBC患者(Act=7.77±2.74,t=3.39,P＜0.01);活动期PBC患者CXCR3 mRNA表达水平(Act=5.41±2.69)明显高于正常对照组(Act=7.16±2.76,t=2.45,P＜0.01)和疾病对照组(Act:7.24±2.75,t=2.53,P＜0.01);缓解期PBC患者CXCR3 mRNA表达水平与正常人及疾病对照组的差异无统计学意义(P＞0.05).结论 PBC患者CXCR3 mRNA表达水平显著高于正常人、疾病对照组和疾病缓解期,提示CXCR3的表达与PBC的发生发展存在一定关联性.     

实时荧光定量PCR测定人肿瘤坏死因子相关凋亡诱导配体基因表达

目的 建立检测人肿瘤坏死因子相关凋亡诱导配体(TRAIL)基因表达含量的实时荧光定量逆转录(FQ-RT)-PCR法,探讨其在健康对照者、乙型病毒性肝炎肝硬化患者及原发性胆汁性肝硬化(PBC)患者外周血单个核细胞(PBMC)中的表达状况.方法 设计TRAIL基因的特异性引物和TaqMan-MGB探针,以β-actin基因为内参,RT-PCR扩增目的 片段.胶同收纯化目的 片段,构建克隆载体作为定最模板,在ABI Prism7000型荧光定量分析仪上进行扩增,建立标准曲线;同时检测30名健康对照者、30例PBC患者及25例乙型病毒性肝炎肝硬化患者外周血PBMC中TRAIL基因的荧光强度和循环阈值,计算样本中TRAIL基因的起始拷贝数.结果 FQ-RT-PCR检测TRAIL mRNA的线性范围为103-106拷贝/ug RNA(r=-0.997);高浓度样本批内和批间变异系数(CV)分别为5.6%和6.3%.低浓度样本批内及批间CV分别为12.5%和14.6%.PBC患者TRAIL mRNA表达量为[(3.3±2.5)×105拷贝ug RNA],高于健康对照组[(0.5±0.2)×105拷贝/ug RNA],两组差异有统计学意义(t=5.994,P<0.01);乙型病毒性肝炎肝硬化患者TRAIL mRNA的表达[(2.1±0.9)×105拷贝/ug RNA]亦高于健康对照组,且差异有统计学意义(t=8.536,P<0.01),而两疾病组间差异无统计学意义(t=1.988,P>0.05).结论 成功建立检测TRAIL mRNA的FQ-RT-PCR法,并初步发现TRAIL mRNA在PBC及乙型病毒性肝炎肝硬化患者外周血PBMC中表达升高,这将对肝硬化肝损伤机制研究提供新的思路.