16S rRNA sequencing analysis: the devil is in the details

ABSTRACT

User-friendly computational tools for 16S ribosomal RNA (rRNA) sequencing analysis enable researchers who are not bioinformaticians to analyze and interpret sequencing data from microbial communities. These tools’ easy-to-use interfaces belie the sophisticated and rapidly-evolving science of their underlying algorithms. When analyzing 16S data from a simple microbiome experiment, we found that superficially unimportant decisions about the bioinformatic pipeline led to results with radically different biological interpretations. We share these results as a cautionary tale whose moral is that, in 16S analysis, the devil is in the details. Wet bench researchers should therefore strongly consider partnering with bioinformaticians or computational biologists when analyzing 16S data.     

Prague women's drinking before and after the 'velvet revolution' of 1989: a longitudinal study

Results are presented of a follow-up study in which a representative sample of 608 Prague women aged 20–49 years in 1987 at first interview was re-interviewed in 1992 3 years after the revolution that ended the 41 years of the Communist era in Czechoslovakia. The average yearly consumption of alcohol in the followed-up female sample increased between 1987–92 from a reported 3.6 litres to 4.8 litres. The percentage of heavier drinkers (with average daily consumption of over 20 g alcohol) increased from 7.2% to 14.0%. The women expressed increased tolerance of drunkenness in their attitudes to drinking. The consumption increase was mainly due to increased drinking frequency of spirits and to increased quantity of beer consumed per occasion. The consumption increase was largest in women working as free-lance and the newly emerging self-employed women; economically inactive women did not increase their consumption. Women who reported a positive impact of the socio-political changes on their personal lives and an expansion of social contacts also reported larger than average consumption increases. A coincidence of stressful, possibly self-inflicted, life events and increased alcohol use was observed and interpreted as probably a two-way influence.     

Predictors of emergent feeding tubes and tracheostomies in amyotrophic lateral sclerosis (ALS)

Predictable decline in ALS makes unplanned gastrostomy and tracheostomy avoidable. We determined whether gastrostomy or tracheostomy insertion during emergent hospitalization is associated with patient or hospital characteristics, changed Medicare policy in 2001, or proximity to specialized ALS care. We performed a retrospective analysis of hospitalizations and procedures for ALS/MND patients in Pennsylvania between 1996 and 2009. We identified predictors of gastrostomy/tracheostomy during emergent hospitalization and trends over time. Patients underwent 1748 gastrostomies and 373 tracheostomies. Thirty-two percent of gastrostomies and 67% of tracheostomies were placed emergently. Emergent hospitalizations involving gastrostomy were more expensive with fewer home discharges. Black patients and Medicaid patients had higher odds of emergent gastrostomy placement. Conversely, academic hospital affiliation decreased odds of emergent gastrostomy or tracheostomy placement (AOR 0.49, AOR 0.37, p 相似文献   

Electromyography activity of selected trunk muscles during cardiopulmonary resuscitation

Background

Understanding trunk muscle activity during chest compression may improve cardiopulmonary resuscitation (CPR) training strategies of CPR or prevent low back pain. This study investigates the trunk muscle activity pattern of chest compression in health care providers to determine the pattern alternation during chest compression.

Methods

Thirty-one experienced health care providers performed CPR for 5 minutes at a frequency of 100 compressions per minute. An electromyography (EMG) system was used to record muscle activity in the first minute, the third minute, and the fifth minute. Electrodes were placed bilaterally over the pectoralis major, latissimus dorsi, rectus abdominis, erector spinae, and gluteus maximus. We calculated the root mean square (RMS) value and maximal amplitude of the EMG activity, median frequency, and delivered force.

Results

The maximal amplitude of EMG of the pectoralis major, erector spinae, and rectus abdominis showed large muscle activity above 45% of maximal voluntary contraction under chest compression. There were no significant differences in the RMS value of one chest compression cycle (RMS_100%) and median frequency for all muscles at the first, third, and fifth minutes. Only gluteus maximus showed significant imbalance. The EMG ratios (erector spinae/rectus abdominis; erector spinae/gluteus maximus) increased significantly over time. The delivered force, compression depth, and number of correct depth decreased significantly over time.

Conclusion

We suggest that the muscle power training for the pectoralis major, erector spinae, and rectus abdominis could be helpful for health care providers. Keeping muscle activity balance of bilateral gluteus maximus and maintaining the same level of EMG ratios might be the keys to prevent low back pain while performing CPR.     

Ultrasonographic and cytologic findings of metastatic cancer in the thyroid gland.

BACKGROUND AND PURPOSE: Cancer metastasizing to the thyroid is not uncommon. Prompt diagnosis and aggressive treatment appear to contribute to better prognosis in some patients. The aim of this study was to determine the clinical manifestations, ultrasonographic and cytologic findings, and outcomes in patients with metastatic thyroid cancer. METHODS: We retrospectively reviewed the medical records, including clinical courses, ultrasonographic and cytologic findings, and outcomes, of 14 patients with metastatic thyroid cancer. RESULTS: There were various primary sites of cancer in our study population, with adenocarcinoma the most common. The sonographic images in five of 12 patients who underwent sonography showed diffusely heterogeneous hypoechoic abnormalities, while the remaining seven patients had nodular lesions. The cytologic appearances of metastatic lesions in the thyroid were characteristic of the primary malignancies. CONCLUSIONS: Most cancer metastatic to the thyroid presented as advanced metastases of primary malignancies. The sonographic appearance alone was not the ideal discriminator, and fine needle aspiration cytology helped define the diagnosis and management strategy.     

Development of a chip-based multiplexed immunoassay using liposomal nanovesicles and its application in the detection of pathogens causing female lower genital tract infections

ObjectiveCervicovaginitis is a highly prevalent disease that is a burden on healthcare globally. Immediate and adequate treatment can eradicate the infection and block subsequent complications. The feasibility of achip-based multiplexed immunoassay using liposomal nanovesicles was tested.Materials and MethodsA multiplexed immunoassay chip containing five antibodies for five pathogens (Chlamydia trachomatis, Escherichia coli, Neisseria gonorrhoeae, Streptococcus agalactiae, and Candida albicans) was established and tested. Four patients with spiking of candidiasis were enrolled. The difference between positive and negative readings was evaluated using the paired Student t test.ResultsThe detection threshold of Candida in this microarray was 100,000 CFU/mL in a vaginal sample, and the time required for the whole procedure was 3 hours. The testing of the four patients showed 100% for both sensitivity and specificity.ConclusionThis microarray chip was a rapid, easy, inexpensive and sensitive tool for detecting female lower genital tract Candida infection in a one-time vaginal sampling process, although the data on the four other pathogens were still unavailable. A larger population study is encouraged to test the validity of this multiplexed immunoassay chip.     

硝苯吡啶与格列本脲相互作用对正常大鼠和高血糖大鼠血糖水平的影响

目的 :研究硝苯吡啶以及硝苯吡啶与格列本脲合用对空腹大鼠和肾上腺素诱发高血糖大鼠血糖水平的影响。方法 :本实验采用葡萄糖氧化酶法测定血糖含量。结果 :硝苯吡啶 2 .5mg/kgig使空腹大鼠血糖水平显著升高(P <0 .0 1 ) ,并加重肾上腺素诱发的高血糖反应。而硝苯吡啶与降糖药格列本脲 0 .9mg/kg合用时不影响空腹大鼠的血糖水平 ,硝苯吡啶对肾上腺素诱发高血糖大鼠灌胃格列本脲后的降血糖作用亦无明显影响。结论 :尽管硝苯吡啶对空腹大鼠以及肾上腺素诱发高血糖大鼠有显著升高血糖的作用 ,但对格列本脲的降血糖作用无明显不良影响     

交沙霉素在中国汉族、维吾尔族及哈萨克族中的药代动力学比较

交沙霉素在中国汉族、维吾尔族及哈萨克族中的药代动力学比较李国昌陈春雁杨明义（新疆石河子医学院第一附属医院药剂科，石河子８３２００８；石河子农学院医院，石河子８３２００３）为探讨交沙霉素（ｊｏｓａｍｙｃｉｎ）在不同民族正常人体内过程，我们用相同的受...     

Evidence for a role of endogenous cannabinoids in the modulation of acute and tonic pain sensitivity

The competitive CB1 receptor antagonist SR141716A was used to test the hypothesis that endogenous cannabinoids modulate tonic pain sensitivity. Pretreatment with the antagonist significantly enhanced the response to a chemical nociceptive stimulus in the formalin test. Postreatment with the antagonist 5 min following the induction of tonic pain produced hyperalgesia during the tonic phase only. These findings suggest that endogenous cannabinoids serve naturally to modulate the maintenance of pain following repeated noxious stimulation.