Efficient screening of predictive biomarkers for individual treatment selection

The development of molecular diagnostic tools to achieve individualized medicine requires identifying predictive biomarkers associated with subgroups of individuals who might receive beneficial or harmful effects from different available treatments. However, due to the large number of candidate biomarkers in the large‐scale genetic and molecular studies, and complex relationships among clinical outcome, biomarkers, and treatments, the ordinary statistical tests for the interactions between treatments and covariates have difficulties from their limited statistical powers. In this paper, we propose an efficient method for detecting predictive biomarkers. We employ weighted loss functions of Chen et al. to directly estimate individual treatment scores and propose synthetic posterior inference for effect sizes of biomarkers. We develop an empirical Bayes approach, namely, we estimate unknown hyperparameters in the prior distribution based on data. We then provide efficient screening methods for the candidate biomarkers via optimal discovery procedure with adequate control of false discovery rate. The proposed method is demonstrated in simulation studies and an application to a breast cancer clinical study in which the proposed method was shown to detect the much larger numbers of significant biomarkers than existing standard methods.     

微血管减压术联合感觉根部分切断术对原发性三叉神经痛患者疼痛评分、生活质量及睡眠状况的影响

目的:探讨微血管减压术(MVD)联合感觉根部分切断术(PSR)对原发性三叉神经痛(TN)患者疼痛评分、生活质量及睡眠状况的影响。方法:回顾性分析2015年2月~2019年3月期间我院收治的80例原发性TN患者的临床资料,根据手术方式的不同将患者分为对照组(n=40,MVD治疗)和研究组(n=40,MVD联合PSR治疗),比较两组患者疼痛评分、生活质量、围术期指标、睡眠状况、并发症发生情况以及复发率。结果:两组患者治疗后视觉疼痛模拟量表(VAS)评分均较治疗前下降,且研究组低于对照组(P<0.05)。两组患者治疗后生活质量量表(SF-36)各维度评分均较治疗前升高,且研究组高于对照组(P<0.05)。两组患者治疗后匹兹堡睡眠质量指数表(PSQI)各项目评分均较治疗前升高,且研究组高于对照组(P<0.05)。研究组住院时间短于对照组,手术时间长于对照组(P<0.05);两组术中出血量比较无统计学差异(P>0.05)。研究组的并发症总发生率低于对照组(P<0.05)。两组随访期间复发率比较差异无统计学意义(P>0.05)。结论:MVD联合PSR治疗原发性TN,虽然手术时间较长,但是在减轻患者疼痛、改善患者生活质量及睡眠状况等方面效果显著,能够降低并发症发生率。     

Interaction of CP levels in maternal and nursery diets,and its effect on performance,protein digestibility,and serum urea levels in piglets

Reduced protein levels in nursery diets have been associated with a lower risk of postweaning diarrhea, but the interaction with CP levels in maternal diet on the performance of the offspring remains unclear. The objective of this study was to determine the effect of protein content in sow gestation and piglet nursery diets on the performance of the piglets until slaughter. This was studied in a 2 × 2 factorial trial (35 sows, 209 piglets), with higher or lower (H or L) dietary CP in sow diets (168 vs 122 g CP/kg) during late gestation. A standard lactation feed was provided for all sows (160 g CP/kg). For both sow treatments, half of the litters received a higher or lower CP in the piglet nursery diet (210 vs 166 g CP/kg). This resulted in four possible treatment combinations: HH, HL, LH and LL, with sow treatment as first and piglet treatment as second letter. For each phase, all diets were iso-energetic and had a similar level of essential amino acids. P_s*p is the p-value for the interaction effect between sow and piglet treatment. In the nursery phase (3.5–9 weeks of age), a tendency toward interaction between piglet and sow treatments with feed efficiency (P_s*p = 0.08) was observed with HH having the highest gain:feed ratio (G:F) (0.74 ± 0.01), LH the lowest (0.70 ± 0.01) and the other two groups intermediate. In the growing-finishing phase, an interaction was observed between the piglet and sow diets with decreased G:F for LH (P_s*p = 0.04) and a tendency toward interaction with increased daily feed intake for LH (P_s*p = 0.07). The sow diet showed a tendency toward a long-lasting effect on the dressing percentage and meat thickness of the offspring, which was higher for the progeny of H sows (P_s < 0.01 and P_s = 0.02, respectively). At 23 weeks, serum urea concentrations tended to be lower for the HH and LL groups (P_s*p = 0.07). Fecal consistency scores were higher at day 10–day 14 after weaning for piglets from L sows (P_s = 0.03 and P_s < 0.01, respectively). At day 7 after weaning, fecal consistency score was higher for piglets fed the higher protein diet (P_p < 0.01). At 8 weeks of age, the apparent total tract digestibility of CP (ATTD_CP) interacted between piglet and sow diet (P_s*p = 0.02), with HH showing the highest digestibility values. In conclusion, the protein levels in sow late-gestation and piglet nursery diets interacted with feed efficiency, ATTD_CP and serum urea concentrations in the nursery phase.     

Using vaginal discharge score (VDS) grading system to evaluate the effect of clinical endometritis on reproductive performance of dairy cows in China

Clinical endometritis (CE) is a major cause in affecting the reproductive performance of dairy cows. The objectives of this study were to ascertain the prevalence of CE and to evaluate the effect of CE on reproductive performance in dairy cows using vaginal discharge score (VDS) grading system. 803 dairy cows were examined by vaginoscope with 4-point VDS at 26 ± 3 days in milk (DIM) and classified into six groups: non-endometritis with VDS 0 (control; CON), endometritis with VDS 1 (MEM), non-treated endometritis with VDS 2 (NTME), treated endometritis with VDS 2 (TME), non-treated endometritis with VDS 3 (NTPE), and treated endometritis with VDS 3 (TPE). Cows in TME and TPE groups were treated with 200 mL of 50% dextrose solution by intrauterine infusion. The prevalence of CE was 33% at 26 ± 3 DIM. Binary logistic regression analysis revealed cows in MEM, NTME and NTPE groups had a less likelihood of first artificial insemination (AI) pregnancy than those in CON group (P < 0.05). Kaplan-Meier survival curves for days open were statistically different (P = 0.004). In Cox regression model, cows in NTME and NTPE groups had a reduced pregnancy rate than those in CON group (P < 0.05). The hazard of pregnancy in NTME group was lower than that in TME group (P = 0.044). Similarly, it was lower for the hazard of pregnancy in NTPE group than in TPE group (P = 0.048). Cows in MEM, NTME, and NTPE groups required more services per pregnancy than those in CON group (P < 0.05). In conclusion, CE examined by the VDS grading system impaired reproductive performance, and mild endometritis with VDS 1 should be treated in the early postpartum period to ameliorate fertility in dairy herds.     

Development and validation of glycolysis-related prognostic score for prediction of prognosis and chemosensitivity of pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with aggressive biological behaviour. Its rapid proliferation and tumour growth require reprogramming of glucose metabolism or the Warburg effect. However, the association between glycolysis-related genes with clinical features and prognosis of PDAC is still unknown. Here, we used the meta-analysis to correlate the hazard ratios (HR) of 106 glycolysis genes from MSigDB by the cox proportional hazards regression analysis in 6 clinical data sets of PDAC patients to form a training cohort, and a single group of PDAC patients from the TCGA, ICGC, Arrayexpress and GEO databases to form the validation cohort. Then, a glycolysis-related prognosis (GRP) score based on 29 glycolysis prognostic genes was established in 757 PDAC patients from the training composite cohort and validated in 267 ICGC-CA validation cohort (all P < .05). In addition, including PADC, the prognostic value was also confirmed in other 7 out of 30 pan-cancer cohorts. The GRP score was significantly related to specific metabolism pathways, immune genes and immune cells in the patients with PADC (all P < .05). Finally, by combining with immune cells, the GRP score also well-predicted the chemosensitivity of patients with PADC in the TCGA cohort (AUC = 0.709). In conclusion, this study developed a GRP score for patients with PDAC in predicting prognosis and chemosensitivity for PDAC.     

Performance of a simplified HEART score and HEART-GP score for evaluating chest pain in urgent primary care

BackgroundChest pain is a common symptom in urgent primary care. The distinction between urgent and non-urgent causes can be challenging. A modified version of the HEART score, in which troponin is omitted (‘simplified HEART’) or replaced by the so-called ‘sense of alarm’ (HEART-GP), may aid in risk stratification.MethodThis study involved a retrospective, observational cohort of consecutive patients evaluated for chest pain at a large-scale, out-of-hours, regional primary care facility in the Netherlands, with 6‑week follow-up for major adverse cardiac events (MACEs). The outcome of interest is diagnostic accuracy, including positive predictive value (PPV) and negative predictive value (NPV).ResultsWe included 664 patients; MACEs occurred in 4.8% (n = 32). For  simplified HEART and HEART-GP, we found C‑statistics of 0.86 (95% confidence interval (CI) 0.80–0.91) and 0.90 (95% CI 0.85–0.95), respectively. Optimal diagnostic accuracy was found for a simplified HEART score ≥2 (PPV 9%, NPV 99.7%), HEART-GP score ≥3 (PPV 11%, NPV 99.7%) and HEART-GP score ≥4 (PPV 16%, NPV 99.4%). Physicians referred 157 patients (23.6%) and missed 6 MACEs. A simplified HEART score ≥2 would have picked up 5 cases, at the expense of 332 referrals (50.0%, p < 0.001). A HEART-GP score of ≥3 and ≥4 would have detected 5 and 3 MACEs and led to 293 (44.1%, p < 0.001) and 186 (28.0%, p = 0.18) referrals, respectively.ConclusionHEART-score modifications including the physicians’ ‘sense of alarm’ may be used as a risk stratification tool for chest pain in primary care in the absence of routine access to troponin assays. Further validation is warranted.Supplementary InformationThe online version of this article (10.1007/s12471-020-01529-4) contains supplementary material, which is available to authorized users.     

Empirical Mode Decomposition and Wavelet Transform Based ECG Data Compression Scheme

ObjectiveIn health-care systems, compression is an essential tool to solve the storage and transmission problems. In this regard, this paper reports a new electrocardiogram (ECG) data compression scheme which employs sifting function based empirical mode decomposition (EMD) and discrete wavelet transform.MethodEMD based on sifting function is utilized to get the first intrinsic mode function (IMF). After EMD, the first IMF and four significant sifting functions are combined together. This combination is free from many irrelevant components of the signal. Discrete wavelet transform (DWT) with mother wavelet ‘bior4.4’ is applied to this combination. The transform coefficients obtained after DWT are passed through dead-zone quantization. It discards small transform coefficients lying around zero. Further, integer conversion of coefficients and run-length encoding are utilized to achieve a compressed form of ECG data.ResultsCompression performance of the proposed scheme is evaluated using 48 ECG records of the MIT-BIH arrhythmia database. In the comparison of compression results, it is observed that the proposed method exhibits better performance than many recent ECG compressors. A mean opinion score test is also conducted to evaluate the true quality of the reconstructed ECG signals.ConclusionThe proposed scheme offers better compression performance with preserving the key features of the signal very well.     

Association between the risk of coronary artery disease in South Asians and a deletion polymorphism in glutathione S-transferase M1

Background: The aim of the present study was to evaluate whether or not an elevated ischaemia-modified albumin (IMA) level provides any additional prognostic information to the validated Thrombolysis In Myocardial Infarction (TIMI) risk score in patients with ST-segment elevation myocardial infarction (STEMI) treated with primary percutaneous coronary intervention (PCI). Methods: One hundred seven consecutive STEMI patients treated with primary PCI were included. The incidence of 30-day death was the prespecified primary end point. Serum IMA was measured immediately at hospital arrival. Results: The incidence of the primary end point was 6.5%. A significant predictive value of IMA in relation to the primary end point was indicated by an area under the ROC curve of 0.71 (p = 0.01). In the multivariate analysis, increased IMA remained a significant predictor of the primary end point after adjustment for TIMI risk predictors (p = 0.019). The area under the ROC curve for the TIMI risk score was 0.68 (p = 0.03). The addition of IMA to the TIMI risk score did not improve its prognostic value (area under the ROC curve 0.60, p = 0.25). Conclusion: IMA levels obtained at admission are a powerful indicator of short-term mortality in STEMI patients treated with primary PCI, but do not seem to be a marker that adds prognostic information to the validated STEMI TIMI risk score.