SimPEL: Simulation‐based power estimation for sequencing studies of low‐prevalence conditions

Power estimations are important for optimizing genotype‐phenotype association study designs. However, existing frameworks are designed for common disorders, and thus ill‐suited for the inherent challenges of studies for low‐prevalence conditions such as rare diseases and infrequent adverse drug reactions. These challenges include small sample sizes and the need to leverage genetic annotation resources in association analyses for the purpose of ranking potential causal genes. We present SimPEL, a simulation‐based program providing power estimations for the design of low‐prevalence condition studies. SimPEL integrates the usage of gene annotation resources for association analyses. Customizable parameters, including the penetrance of the putative causal allele and the employed pathogenic scoring system, allow SimPEL to realistically model a large range of study designs. To demonstrate the effects of various parameters on power, we estimated the power of several simulated designs using SimPEL and captured power trends in agreement with observations from current literature on low‐frequency condition studies. SimPEL, as a tool, provides researchers studying low‐frequency conditions with an intuitive and highly flexible avenue for statistical power estimation. The platform‐independent “batteries included” executable and default input files are available at https://github.com/precisionomics/SimPEL .     

Trace and evaluation systems for health services quality in rural and remote areas: a systematic review

Aim

To provide a systematic review of the existing theory, framework, systems and instruments for tracing and evaluating quality in rural health services.

Subjects and methods

We searched six electronic databases up to March 2016. Observational studies of quality assessment of rural health services using theoretical models were included. Ekman’s scale was used to evaluate the quality of the included studies.

Results

A total of 18 studies, published between 2001 and 2015, met the inclusion criteria. The corresponding authors for most of them (7, 44%) are from Chinese institutions and three (3, 17%) from Australian institutions. Five studies (28%) focused on township hospitals. Primary health care quality was reported in five studies (28%), followed by clinical service in four (22%). More than half of the studies (61%) were considered of high quality, and the remainder was of moderate quality. These studies applied 16 theoretical systems, including the model/pattern (4, 25%), method/tool (7, 44%) and framework of the theory (5, 31%). Most of the theoretical models (14, 88%) obtained positive observations. In addition, the conceptual model (6, 36%) and TOPSIS method (2, 13%) were more frequently reported.

Conclusion

Although most of the current studies were considered to have high-quality and positive results, there were limitations in the number of publications and research on theoretical systems. The lacks of unified standards and comprehensive evaluation are important issues that need to be pointed out and resolved.

     

Psychometric validation of the SF-36<Superscript>®</Superscript> Health Survey in ulcerative colitis: results from a systematic literature review

Purpose

To conduct a systematic literature review of the reliability, construct validity, and responsiveness of the SF-36^® Health Survey (SF-36) in patients with ulcerative colitis (UC).

Methods

We performed a systematic search of electronic medical databases to identify published peer-reviewed studies which reported scores from the eight scales and/or two summary measures of the SF-36 collected from adult patients with UC. Study findings relevant to reliability, construct validity, and responsiveness were reviewed.

Results

Data were extracted and summarized from 43 articles meeting inclusion criteria. Convergent validity was supported by findings that 83% (197/236) of correlations between SF-36 scales and measures of disease symptoms, disease activity, and functioning exceeded the prespecified threshold (r ≥ |0.40|). Known-groups validity was supported by findings of clinically meaningful differences in SF-36 scores between subgroups of patients when classified by disease activity (i.e., active versus inactive), symptom status, and comorbidity status. Responsiveness was supported by findings of clinically meaningful changes in SF-36 scores following treatment in non-comparative trials, and by meaningfully larger improvements in SF-36 scores in treatment arms relative to controls in randomized controlled trials. The sole study of SF-36 reliability found evidence supporting internal consistency (Cronbach’s α ≥ 0.70) for all SF-36 scales and test–retest reliability (intraclass correlation coefficient ≥0.70) for six of eight scales.

Conclusions

Evidence from this systematic literature review indicates that the SF-36 is reliable, valid, and responsive when used with UC patients, supporting the inclusion of the SF-36 as an endpoint in clinical trials for this patient population.

     

Comparative Study of Metal Accumulation in Three Fish Species (<Emphasis Type="Italic">Silurus asotus,Cyprinus carpio</Emphasis>, and <Emphasis Type="Italic">Carassius auratus auratus</Emphasis>) from the Jinsha and Tuo Rivers Located Upstream of the Yangtze River,China

Poland is one of the countries distinguished by a long and colorful past. Undergoing numerous turbulent socio-economic changes forced by the course of history, Poland is now one of the member states of the European Union. Experiencing low water quantity and high contamination levels in surface waters, Poland is following other EU countries in the effort to reach a “good” water status. Herein are presented impacts of changes in Polish history on water legislation, management, and research, as well as explanations for the perceptible split between engineering and scientific approaches to the aquatic issues. Drawbacks caused by unsatisfactory state research funding for the sciences and division of the water related contemporary scientific interests are also discussed.     

谷氨酰胺联合益生菌治疗失代偿肝硬化患者的临床研究

目的观察谷氨酰胺联合益生菌对失代偿肝硬化患者的疗效与安全性。方法收集本院失代偿肝硬化患者78例,随机分为2组,每组39例:对照组用常规治疗;在常规治疗的基础上,试验组用谷氨酰胺联合益生菌治疗,复方谷氨酰胺肠溶胶囊,每次750 mg;枯草杆菌二联活菌肠溶胶囊口服,每次250 mg,两药均每天3次,连用4周。治疗前后,测定2组的肠黏膜通透性指标、肝功能指标、疗效和药物不良反应(ADR)发生率。结果治疗后,试验组与对照组的尿乳果糖/甘露醇比值分别是0.09±0.06,0.12±0.08,这2组的血清白细胞介素-8水平分别是(15.02±3.69),(18.45±4.10)ng·L^-1,这2组的血清谷丙转氨酶水平分别是(24.61±14.29),(36.82±15.67)U·L^-1,上述3个指标在组间比较差异均有统计学意义(均P<0.05)。对照组和试验组的改善率分别为71.80%,92.31%,差异有统计学意义(P<0.05)。对照组和试验组的ADR发生率分别为15.38%(6例/39例),20.51%(8例/39例),组间比较差异无统计学意义(P>0.05)。结论谷氨酰胺联合益生菌对失代偿肝硬化患者的治疗效果确切,有助于降低肠黏膜通透性和提高肝功能;且不增加ADR发生率。     

影响抗生素微生物检定法(管碟法)测定准确性的常见原因分析

目的 总结抗生素微生物检定法(管碟法)中影响测定结果准确性的常见系统误差并加以控制。方法 梳理10余年来中检院仲裁复验的案例,对共性问题进行整理,找出可能原因,并采用单一变量实验设计的方式加以确证。结果 估计效价和浓度比的错误计算、点样顺序和点样时间规范性和熟练程度、试验标准菌株的变异均会对管碟法测定结果产生影响。结论 通过细化实验操作规范,可以避免或尽量消除此类系统误差的影响。