Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols

Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design.

Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome

BACKGROUND

The gut microbiome is altered in several neurologic disorders, including Parkinson's disease (PD).

OBJECTIVES

The aim is to profile the fecal gut metagenome in PD for alterations in microbial composition, taxon abundance, metabolic pathways, and microbial gene products, and their relationship with disease progression.

METHODS

Shotgun metagenomic sequencing was conducted on 244 stool donors from two independent cohorts in the United States, including individuals with PD (n = 48, n = 47, respectively), environmental household controls (HC, n = 29, n = 30), and community population controls (PC, n = 41, n = 49). Microbial features consistently altered in PD compared to HC and PC subjects were identified. Data were cross-referenced to public metagenomic data sets from two previous studies in Germany and China to determine generalizable microbiome features.

RESULTS

We find several significantly altered taxa between PD and controls within the two cohorts sequenced in this study. Analysis across global cohorts returns consistent changes only in Intestinimonas butyriciproducens. Pathway enrichment analysis reveals disruptions in microbial carbohydrate and lipid metabolism and increased amino acid and nucleotide metabolism in PD. Global gene-level signatures indicate an increased response to oxidative stress, decreased cellular growth and microbial motility, and disrupted intercommunity signaling.

CONCLUSIONS

A metagenomic meta-analysis of PD shows consistent and novel alterations in functional metabolic potential and microbial gene abundance across four independent studies from three continents. These data reveal that stereotypic changes in the functional potential of the gut microbiome are a consistent feature of PD, highlighting potential diagnostic and therapeutic avenues for future research. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

0196 Differences in Sleep Duration and Alertness Among Internal Medicine Interns Comparing Intensive Care Unit to General Medicine Rotations: A Secondary Analysis of the ICOMPARE Trial

Introduction

Little is known about the impact of specific rotations on medical residents’ sleep. The purpose of this analysis was to examine the difference in sleep duration and alertness among internal-medicine resident interns during intensive care unit (ICU) compared to general medicine (GM) rotations.

Methods

This is a secondary report of a randomized non-inferiority trial of 63 United States internal-medicine residency programs. Programs were assigned to either standard duty-hour (80h workweek/16h shifts) or flexible (80h workweek/no shift-length limit) policies. Interns were followed for 2 weeks during either a GM or ICU rotation. The primary outcome was sleep duration/24h (actigraphy). Secondary outcomes were sleepiness (Karolinska Sleepiness Scale [KSS]) and alertness (number of Brief Psychomotor Vigilance Test [PVT-B] lapses). Data were averaged across days (thirteen 24-hour periods). Linear mixed-effect models with random program intercept were used to determine the association between each outcome by rotation, controlling for age, sex, and policy followed.

Results

N=386 interns were included (mean age 27.9±2.1y, 194 (50.3%) males), with n=261 (67.6%) in GM, and n=125 (32.4%) in ICU. Average sleep duration was 7.00±0.08h and 6.84±0.10h for GM and ICU respectively (p=.09; 95%CI -0.02;0.33h). Percent of days with self-reports of excessive sleepiness were significantly more likely for ICU vs GM from 12am-6am (ICU: 20.2%; GM: 12.5%) and 6am-12pm (ICU: 20.5%; GM: 14.3%). GM had significantly more days with no excessive sleepiness (GM: 40.5%; ICU: 28.1%). Average KSS was 4.8±0.1 for both GM and ICU (p=.60; 95%CI -0.18;0.32). Average number of PVT-B lapses were 5.5±0.5 and 5.7±0.7 for GM and ICU respectively (p=.83; 95%CI -1.48;1.18 lapses). There were no significant differences in PVT-B response speed or false starts between rotations.

Conclusion

Interns in ICU may experience more excessive sleepiness compared to GM interns, especially in early morning hours. However, sleep duration and alertness were not significantly different between rotations.

Support

Funded by the National Heart, Lung, and Blood Institute and American Council for Graduate Medical Education

0261 A Randomized Trial on The Effects of Standard and Flexible Duty-Hour Rules on Intern Sleep and Alertness

Introduction

Duty hour regulations affect resident sleep, education, and patient care in complex ways. We performed a national cluster-randomized trial (iCOMPARE) in 63 internal medicine residency programs comparing the effects of the 2011 duty-hour standards to a more flexible set of duty hour rules characterized by maintaining an 80-hour workweek but without limits on shift length or mandatory time off between shifts, relative to patient mortality, intern educational outcomes, and intern sleep and alertness.

Methods

In the sleep and alertness sub-study, sleep duration and morning sleepiness and alertness were assessed with actigraphy, the Karolinska Sleepiness Scale, and a 3-minute Psychomotor Vigilance Test (PVT-B) for 14 days in 193 interns from 6 standard programs and 205 interns from 6 flexible programs.

Results

During the 14-day study periods, interns in standard and flexible programs averaged 7.03h sleep/24h (95% confidence interval [CI] 6.78h, 7.27h) and 6.85h sleep/24h (95% CI 6.61h, 7.10h), respectively. Sleep duration (difference between arms of -0.17h/24h; 1-sided lower 95% confidence limit -0.45h; NIM -0.5h; P=0.02 for noninferiority) and KSS sleepiness (difference 0.12 points; 1-sided upper 95% confidence limit 0.31 points; NIM 1 point; P<0.001) were noninferior in flexible versus standard programs. We could not establish noninferiority for PVT-B alertness (difference -0.3 lapses; 1-sided upper 95% confidence limit 1.6 lapses; NIM 1 lapse; P=0.10). Based on analyses by shift type, sleep duration was 1.77h shorter on days when interns in flexible programs finished an overnight shift relative to a regular day shift (p<.001), with significant decreases in subjective and objective alertness, and frequent reports of excessive sleepiness, especially between 12am and 6am.

Conclusion

There were no signs of relevant chronic sleep loss across shifts in interns in flexible programs relative to their standard program counterparts. Interns were able to compensate for the sleep lost during extended overnight shifts by increasing sleep duration on nights prior to day shifts, night shifts, and days off. Increased sleepiness and reduced alertness of interns following extended overnight shifts need to be mitigated and suggest a role for fatigue-risk management programs.

Support

Supported by NHLBI grants U01HL125388 and U01HL126088 and grants from the ACGME.

Sexual health innovations in undergraduate medical education

Recent national and global initiatives have drawn attention to the importance of sexual health to individuals' well-being. These initiatives advocate enhancement of efforts to address this under-represented topic in health professions curricula. University of Massachusetts Medical School (UMMS) has undertaken a comprehensive effort to develop an integrated curriculum in sexual health. The UMMS project draws upon the expertise of a multidisciplinary faculty of clinicians, basic scientists, a medical ethicist, and educators. This article describes the project's genesis and development at UMMS, and reports on three innovations in sexual health education implemented as part of this endeavor.

Tumor size on computed tomography scans: is one measurement enough?

BACKGROUND

Bidimensional tumor measurements are used routinely as surrogates for tumor volume. The purpose this study was to determine whether there is any added benefit in bidimensional or tridimensional measurements over a unidimensional measurement.

METHODS

Sixty-nine colorectal hepatic metastases on 19 computed tomography scans (1-8 lesions per scan) from 9 patients were analyzed. Five patients contributed 2-4 scans each (mean, 3 scans). The standard volume of these lesions was determined by the "summation of areas" technique. The maximum axial dimension, the product of the greatest axial dimensions, and several volume estimates (based on the volumes of a sphere, an ellipsoid, and a cube) each were correlated with the standard volume.

RESULTS

The maximum axial dimension and the product of the greatest axial dimensions correlated equally with tumor volume (correlation coefficient = 0.93). Surrogate measures based on the equations for a sphere and an ellipsoid underestimated tumor volume, whereas the equation for a cube overestimated volume.

CONCLUSIONS

When reporting tumor size, there is no significant added benefit in reporting bidimensional or tridimensional measurements over the maximum axial dimension.

Paraspinal muscle hematoma after electromyography

There have been few reports of complications related to electromyography. Needle examination of certain muscles is sometimes avoided in patients taking anticoagulant agents, although no clear guidelines have been established. We describe a patient who was not receiving an anticoagulant and developed a large paraspinal muscle hematoma after routine electromyography. Subsequently, all patients who underwent paraspinal muscle electromyography and were diagnosed with radiculopathy at our institution over a 14-month period were reviewed. From this group, 17 patients were identified who had also underwent MRI of the appropriate spinal levels within 1 week after the needle examination. These images were reviewed for evidence of paraspinal muscle hematomas. Four small hematomas were identified in four different patients. None of these were radiologically significant compared with the large hematoma described in the case report. Radiologically apparent paraspinal hematomas after electromyography are an unusual complication of needle examination and do not appear to have any clinical significance. Nevertheless, the presence of these lesions justifies caution when considering electromyography of paraspinal and other deeper muscles in anticoagulated patients.

Perturbation of target-directed neurite outgrowth in embryonic CNS co-cultures grown in the presence of ethanol

Studies were conducted to determine the influence of ethanol on target-directed fiber outgrowth in culture, using embryonic chick spinal cord-muscle, and fetal rat septal-hippocampal co-cultured explants. Process extension from the spinal cord and septal explants in control cultures was selectively oriented toward the appropriate target tissue. Ethanol in the culture medium (500 mg/dl) eliminated this target-oriented outgrowth in both systems, although the overall extent of neurite outgrowth was not affected. In an effort to further characterize the source of this disruption, target explants were grown alone, with and without ethanol, and the target-conditioned culture media was subsequently harvested and placed on newly plated spinal cord or septal explants, to determine whether ethanol decreased the target production of soluble substances. To determine whether deposition of substrate-bound materials by the target tissue was affected by ethanol, spinal cord or septal explants were plated in wells which had previously been occupied by the appropriate target tissue. These studies revealed that ethanol significantly inhibited production of soluble and substrate-bound materials by muscle explants, but not by hippocampal explants. It was concluded that the ethanol-induced loss of target-directed neurite outgrowth in the spinal cord explants could be accounted for primarily by the attenuated production of neurotropic/neurotropic substances by the muscle tissue. The loss of target-directionality in the septal explants appeared to be due to other factors, possibly related to ethanol-induced compromise of the capacity of the septal neurons to respond appropriately to target-derived neurotrophic/neurotropic substances. The implications of these results for the fetal alcohol syndrome are considered.

Evaluation of an asymmetric screen-film system for chest radiography

To evaluate the potential utility of an asymmetric screen-film system for chest radiography, its image quality and detail visibility compared with a conventional screen-film system are investigated. The basic imaging properties were evaluated by measuring Hurter and Driffield curves, resolution properties, and noise Wiener spectra. The visibility of simulated anatomical and pathological details in radiographs of a chest phantom and normal anatomy in chest radiographs of patients were evaluated subjectively. The dynamic range of each system is comparable, though the asymmetric screen-film system can provide an advantage over the conventional system due to a relative dose reduction of approximately 35% and higher resolution properties at high optical densities. The noise level of the asymmetric screen-film system is slightly greater at low optical densities and much greater at high optical densities. However, the visibility of lung details with the asymmetric screen-film system is slightly superior to the conventional screen-film system despite the increase in noise. Mediastinal and retrodiaphragmatic details are similar, though marginally superior with the asymmetric screen-film system. It is concluded that the asymmetric screen-film system provided slightly superior image quality to the conventional screen-film system for chest radiography, provided the average lung density is maintained at a higher level than is customary with conventional systems.

Development of a digital duplication system for portable chest radiographs

To provide high-quality duplicate chest images for the intensive care units, we have developed a digital duplication system in which film digitization is performed in conjunction with nonlinear density correction, contrast adjustment, and unsharp mask filtering. This system provides consistent image densities over a wide exposure range and enhancement of structures in the mediastinum and upper abdominal areas, improving visibility of catheters and tubes. The image quality is often superior to that of the original radiograph and is more consistent from day to day. Repeat rates for portable chest radiographs have been reduced by more than a factor of two since implementation of digitization in December 1991, and the number of repeat examinations caused by exposure errors have been substantially reduced.

Incongruous item generation effects: a multiple-cue perspective

In a series of studies, generation effects were obtained under encoding conditions designed to induce incongruous, unrelated item generation. Experiments 1 and 2, using free- and cued-recall measures, respectively, provided evidence that this unrelated generation effect was due to response-specific processing. Experiment 3 demonstrated a lack of relation between free recall and indices of clustering. A preliminary protocol study suggested that Ss generate multiple items in their search for appropriate unrelated responses. In Experiments 4 and 5, conditions designed to produce more extensive multiple generations demonstrated enhanced free recall. These results supported a multiple-cue account of facilitated recall for incongruous item generation. The multiple-cue perspective is consistent with traditional conceptualizations of memory, such as the principle of congruity, and contemporary distinctions between cue-target relational and item-specific processing.

Incongruous item generation effects: a multiple-cue perspective

In a series of studies, generation effects were obtained under encoding conditions designed to induce incongruous, unrelated item generation. Experiments 1 and 2, using free- and cued-recall measures, respectively, provided evidence that this unrelated generation effect was due to response-specific processing. Experiment 3 demonstrated a lack of relation between free recall and indices of clustering. A preliminary protocol study suggested that Ss generate multiple items in their search for appropriate unrelated responses. In Experiments 4 and 5, conditions designed to produce more extensive multiple generations demonstrated enhanced free recall. These results supported a multiple-cue account of facilitated recall for incongruous item generation. The multiple-cue perspective is consistent with traditional conceptualizations of memory, such as the principle of congruity, and contemporary distinctions between cue-target relational and item-specific processing.

Comparison of fixed and adjustable window width and level settings in the CT evaluation of diffuse lung disease

OBJECTIVE

The purpose of this investigation was to assess the utility of allowing free adjustment of window width and level in comparison with the use of a fixed lung window in the CT evaluation of diffuse lung disease.

MATERIALS AND METHODS

Six radiologists each judged 36 cases (28 diffuse lung disease and 8 normal) using a standardized form. In half of the sessions, images were viewed in a fixed lung window (level = -500 HU; width = 2,000 HU). In the other sessions, the observer was able to adjust the window and level freely while viewing the images. Each case was seen twice in separate sessions: once in a fixed lung window and once with window width and level adjusted by the reader. A variety of diagnostic features were evaluated using a 5 point scale. These included visibility of fine lung structures, abnormalities of the lung parenchyma, and overall evaluation of the lung.

RESULTS

The visibility of lung structures was not improved with adjustable window settings. Receiver operating characteristic (ROC) analysis showed fixed windows to be superior to adjustable windows for overall evaluation of the cases [fixed A(z) = 0.90, adjustable A(z) = 0.84, p < 0.05, jackknife method]. Time to rate each case was increased by 15% with window width and level adjustment.

CONCLUSION

Free adjustment of window width and level produced no improvement in reader performance over that achieved with fixed window width and level.

Clinical experience with an advanced laser digitizer for cost-effective digital radiography

Film digitization has not been widely pursued in clinical settings mainly because of perceived limitations involving film latitude and image quality. However, a high-quality laser digitizer can be combined with wide-latitude film and specially developed digital processing techniques to achieve image quality comparable or superior to that of storage phosphor computed radiography (SPR) over a wide range of exposure. This film digitization system provides the operational advantages of digital radiography, such as consistent image density, high-quality inexpensive duplicates, and digital storage and retrieval capability. The reliability and monetary costs of the system also compare favorably with those of SPR. In the long term, technologies that employ reusable plates and do not require chemical processing to produce diagnostic images may well replace screen-film systems. Presently, however, film digitization remains a practical and cost-effective approach to digital radiography.

Laser alignment system for high-quality portable radiography

In portable radiography, image quality is degraded by scattered radiation. Use of an accurately aligned, antiscatter grid can provide consistently high image quality, but the necessary precision for grid alignment is difficult to achieve with conventional techniques. The authors developed a simple laser alignment method for bedside radiography. A compact laser device is mounted on the collimator housing of a mobile radiography machine, so that the laser beam is precisely parallel to the central x-ray beam. A small reflector device, which attaches to the edge of the grid cassette, indicates beam centering and alignment in a clear, intuitive way. In clinical use, the laser alignment technique provided uniformly high image quality, equivalent to that of fixed equipment. The system has the advantages of being simple to use and inexpensive to implement with existing equipment.

Direct comparison of conventional and computed radiography with a dual-image recording technique

To compare the image quality of computed radiographic (CR) with conventional screen-film images, the authors used a dual-image recording technique. Images were simultaneously acquired with a conventional screen-film combination and a storage-phosphor imaging plate loaded into a single cassette. Wiener spectra and modulation transfer function were compared for both image types. A preliminary observer performance test was conducted with chest images obtained with the dual-image recording technique on portable and fixed equipment. Analysis of physical parameters and observer test results suggests that the conventional screen-film system can provide slightly superior image quality, although the CR system has some advantage in bedside applications.

Physical and clinical evaluation of new high-strip-density radiographic grids

The imaging performance of new high-strip-density (HSD) grids having 57 lines/cm was compared with that of conventional low-strip-density (LSD) grids having 33 or 40 lines/cm. The unique advantage of HSD grids is that, under most standard radiographic conditions, the grid lines are not noticeable on the final image, even if the grid is stationary. This is due to the combined effect of the high fundamental spatial frequency of HSD grids, the modulation transfer function of screen-film systems and of the human visual system, and scattered radiation. Monte Carlo simulation studies, phantom images, and clinical evaluation indicate that HSD grids can provide contrast improvement factors and Bucky factors that are comparable to or slightly better than those obtained with LSD grids. Therefore, it may now be possible to eliminate moving Bucky trays from radiographic tables and fluoroscopic devices.

Factors associated with cigaret smoking in elementary school children

A survey of 625 elementary school children in an urban area for substance use, specifically, cigarets, alcohol and drugs, and the social factors associated with such use, revealed 38 admitted smokers in this age range, strongly influenced by parents, siblings and peers who smoked. Cigaret use was also associated with drug and alcohol use. These findings corroborate those from studies of teenagers who smoke, showing that peer pressure is not the sole factor in starting to smoke, as several other studies have claimed. In elementary school children, smoking is rare enough to be considered an early indicator of social deviation.