A semiparametric model for between-subject attributes: Applications to beta-diversity of microbiome data

The human microbiome plays an important role in our health and identifying factors associated with microbiome composition provides insights into inherent disease mechanisms. By amplifying and sequencing the marker genes in high-throughput sequencing, with highly similar sequences binned together, we obtain operational taxonomic units (OTUs) profiles for each subject. Due to the high-dimensionality and nonnormality features of the OTUs, the measure of diversity is introduced as a summarization at the microbial community level, including the distance-based beta-diversity between individuals. Analyses of such between-subject attributes are not amenable to the predominant within-subject-based statistical paradigm, such as t-tests and linear regression. In this paper, we propose a new approach to model beta-diversity as a response within a regression setting by utilizing the functional response models (FRMs), a class of semiparametric models for between- as well as within-subject attributes. The new approach not only addresses limitations of current methods for beta-diversity with cross-sectional data, but also provides a premise for extending the approach to longitudinal and other clustered data in the future. The proposed approach is illustrated with both real and simulated data.

[Application and progress of artificial intelligence technology in gastric cancer diagnosis and treatment]

Artificial intelligence (AI) is one of the most rapidly evolving fields in biomedicine during the past decade. Represented by radiomics, machine learning and deep neural network, AI has been increasingly favored by researchers due to its ability to obtain feature information and discover the potential relationship between data and medical outcomes from high-throughput medical data. The incidence and mortality of gastric cancer (GC) has remained high in China. Through combining AI technology with medical examination such as endoscopy, imaging, pathological examination and sequencing, clinical researchers have made great progress in the auxiliary diagnosis, disease staging, prognosis and curative effect prediction of patients with GC. Although the intervention of AI in the medical industry has greatly improved the effective utilization of high-throughput data and accelerated the intelligent process of disease diagnosis and treatment, a number of problems has been raised in medical ethics, patient privacy and the legal status of medical AI at the same time. In the future, rational planning and management of AI technology will provide a strong impetus to promote the development of medicine and reshape the medical industry.

Main COVID-19 information sources in a culturally and linguistically diverse community in Sydney, Australia: A cross-sectional survey

OBJECTIVE

Describe COVID-19 information-seeking experiences for culturally and linguistically diverse groups in Sydney, Australia.

METHODS

Cross-sectional survey, translated into 11 languages; participants recruited from March 21 to July 9, 2021. Regression models identified factors associated with difficulty finding easy-to-understand COVID-19 information.

RESULTS

Across 708 participants (88% born overseas, 31% poor English proficiency), difficulty finding easy-to-understand COVID-19 information was rated 4.13 for English (95%CI: 3.85-4.41) and 4.36 for non-English language materials (95%CI: 4.07-4.66) (1 easy to 10 hard). Participants who were older (p < 0.001), had inadequate health literacy (p < 0.001), or poor English proficiency (p < 0.001) found it harder to find easy-to-understand English-language COVID-19 information. Those who had greater difficulty finding easy-to-understand non-English COVID-19 information were younger (p = 0.004), had poor English proficiency (p < 0.001), were university-educated (p = 0.05), and had spent longer living in Australia (p = 0.001). They were more likely to rely on friends and family for COVID-19 information (p = 0.02). There was significant variation in information-seeking experiences across language groups (p's < 0.001).

CONCLUSIONS

Easy-to-understand and accessible COVID-19 information is needed to meet the needs of people in culturally and linguistically diverse communities.

PRACTICE IMPLICATIONS

COVID-19 communication efforts must involve working alongside these communities to leverage existing communication channels and tailor messages.

Observation of a State X(2600) in the π^{+}π^{-}η' System in the Process J/ψ→γπ^{+}π^{-}η'

Based on (10087±44)×10^{6}  J/ψ events collected with the BESIII detector, the process J/ψ→γπ^{+}π^{-}η^{'} is studied using two largest decay channels of the η^{'} meson, η^{'}→γπ^{+}π^{-} and η^{'}→ηπ^{+}π^{-}, η→γγ. A new resonance, which we denote as the X(2600), is observed with a statistical significance larger than 20σ in the π^{+}π^{-}η^{'} invariant mass spectrum, and it has a connection to a structure around 1.5  GeV/c^{2} in the π^{+}π^{-} invariant mass spectrum. A simultaneous fit on the π^{+}π^{-}η^{'} and π^{+}π^{-} invariant mass spectra with the two η^{'} decay modes indicates that the mass and width of the X(2600) state are 2618.3±2.0_{-1.4}^{+16.3}  MeV/c^{2} and 195±5_{-17}^{+26}  MeV, where the first uncertainties are statistical, and the second systematic.

[Pay close attention to the current characteristics and development trend of severe acute hepatitis with unknown etiology in children worldwide]

In the past, acute hepatitis of unknown etiology in children was sporadic. However, during the last three weeks, there has been a trend of short-term outbreak around the world. As of May 3, 2022, at least 228 cases had been reported in about 20 countries and regions. The main clinical manifestations of the children included abdominal pain, diarrhea, vomiting, jaundice, and hepatomegaly. The liver functions including alanine aminotransferase and total bilirubin increased sharply. About 8.8% of the children needed liver transplantation. The etiology is not clear, but adenovirus type 41 is currently considered to be the most likely cause. Clinicians should keep alert to acute hepatitis of unknown etiology in children, strengthen epidemic surveillance, clinical treatment, and carry out necessary health education.

[Treatment effects of sandwich-shaped resection and cheiloplasty applied in macrocheilia secondary to arteriovenous malformations]

To summarize the clinical experience of sandwich-shaped resection and cheiloplasty in the treatment of macrocheilia secondary to arteriovenous malformation, and to observe its clinical efficacy and complications. The clinical data of 27 patients with macrocheilia secondary to arteriovenous malformation who received surgical treatment from January 2018 to October 2020 in Linyi Cancer Hospital were retrospectively analyzed. There were 14 males and 13 females. The median age was 4.5 years (ranged from 2 to 57 years). There were 18 cases of upper lip and 9 cases of lower lip. All patients had received interventional embolization sclerotherapy for 5 to 10 times before surgery with unsatisfied effect. There was no obvious improvement in the appearance,whereas 3 cases progressed presenting as abnormal enlargement. Sandwich-shaped resection and cheiloplasty was performed in all the patients. Histopathological examinations confirmed arteriovenous malformations in all 27 cases. Twenty-six patients received one course of operation and one received two courses. Partial mucosal necrosis occurred in 1 case and healed after dressing change, while the rest healed by first intention. Local recurrence occurred in 2 cases within 6 months after operation. A four-level standard was used for long-term evaluation, and 24 cases got grade Ⅲ (good), three cases got grade Ⅱ (moderate) after 1 to 3 years of follow-up. Sandwich-shaped resection and cheiloplasty can achieve good long-term efficacy with excellent appearance and function. Due to its advantages of hidden incision and three-dimensional resection and reservation, it is worthy of further clinical promotion.

[Carotid intraplaque neovascularization is correlated with the risk of revascularization following percutaneous coronary intervention]

OBJECTIVE

To investigate the correlation of intraplaque neovascularization (IPN) detected by carotid contrast-enhanced ultrasound (CEUS) with revascularization in patients following percutaneous coronary intervention (PCI).

METHODS

This study was conducted among 105 patients who were followed up for more than 12 months after PCI. All the patients received CEUS examination for assessment of carotid plaque formation and IPN, which were compared between patients with revascularization (REV group, n=27) and those without revascularization (N-REV group, n=78). ROC curve was used to analyze the diagnostic efficacy of CEUS for predicting revascularization. Univariate and multivariate logistic regression analyses were performed to identify the risk factors associated with revascularization.

RESULTS

In the REV group, the IPN score was 0 in 1 (3.7%) patient, 1 in 8 (29.6%) patients, 2 in 15 (55.6%) patients and 3 in 3 (11.1%) patients. Significant differences were noted between REV and N-REV groups in plaque length (15.70±6.93 vs 12.10±6.64, P < 0.05), maximum plaque thickness (3.69±1.12 vs 3.14±1.18, P < 0.05) and IPN (1.74±0.71 vs 0.87±0.63, P < 0.001). IPN score was identified as an independent risk factor for revascularization in patients following PCI, and at the cutoff value of 1.5, its sensitivity, specificity, positive predictive value, and negative predictive value for predicting the occurrence of revascularization were 74%, 89%, 69%, and 91%, respectively, with an AUC of 0.848 (95% CI: 0.703-0.905, P < 0.001).

CONCLUSION

CEUS allows noninvasive and semi-quantitative assessment of neovascularization in carotid artery plaques, and IPN detected by CEUS is correlated with the risk of revascularization in patients following PCI.

[Disease spectrum analysis of children with inherited metabolic diseases detected by gas chromatography-mass spectrometry of urinary organic acids]

Objective: To investigate the spectrum of amino acid, organic acid, and fatty acid oxidative metabolic diseases in children diagnosed by detecting urinary organic acid levels using gas chromatography-mass spectrometry. Methods: From January 2005 to December 2021, clinical data of 2 461 children diagnosed with inherited metabolic diseases (IMD) by gas chromatography-mass spectrometry, in combination with tandem mass spectrometry and genetic testing in Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine were retrospectively analyzed. Results: Among 2 461 children, 1 446 were male and 1 051 were female. A total of 32 types of IMD were detected among 2 461 patients, which included 10 amino acid disorders in 662 cases (26.9%), 6 common diseases were hyperphenylalaninemia, citrin deficiency, ornithine carbamoyltransferase deficiency, maple syrup urine disease, alkaptonuria, and tyrosinemia-I, 17 types of organic acidemias in 1 683 cases (68.4%), 6 common diseases were methylmalonic acidemia, propionic acidemia, valeric acidemia-type Ⅰ, isovaleric acidemia, 3-methylcrotonyl-CoA carboxylase deficiency and multiple carboxylase deficiency and 5 fatty acid β oxidative defects in 116 cases (4.7%), 2 common diseases were multiple acyl-CoA dehydrogenase deficiency and short-chain acyl-CoA dehydrogenase deficiency). Conclusion: Among the diseases diagnosed by analyzing urinary organic acid profiling with gas chromatography-mass spectrometry, the most common are organic acidemias, followed by amino acid disorders and fatty acid oxidation defects.

[Development of a Ranking Tool for Scientificity, Transparency and Applicability of Clinical Practice Guidelines]

Objective: To address the limitations of existing methods and tools for evaluating clinical practice guidelines, we aimed to develop a comprehensive instrument focusing on the three main dimensions of guideline development: scientificity, transparency, applicability. We will use it to rank the guidelines according to the scores. We abbreviated it as STAR, and its reliability, validity and usability were also tested. Methods: A multidisciplinary expert working group was set up, including methodologists, statisticians, journal editors, medical professionals, and others. Scoping review, Delphi methods and hierarchical analysis were used to determine the final checklist of STAR. Results: The new instrument contained 11 domains and 39 items. Intrinsic reliability of each domain was indicated by Cronbach's α coefficient, with a average value of 0.646. The Cohen's kappa coefficients for methodological evaluators and clinical evaluators were 0.783 and 0.618. The overall content validity index was 0.905. The R2 for the criterion validity analysis was 0.76. The average score for usability of the items was 4.6, and the mean time spent to evaluate each guideline was 20 minutes. Conclusion: The instrument has good reliability, validity and evaluating efficiency, and can be used for evaluating and ranking guidelines more comprehensively.

[Safety and effectiveness of esophagojejunostomy through extracorporeal versus intracorporeal methods after laparoscopic total gastrectomy]

Objective: To compare the safety and effectiveness of esophagojejunostomy (EJS) through extracorporeal and intracorporeal methods after laparoscopic total gastrectomy (LTG). Methods: A retrospective cohort study was carried out. Clinicopathological data of 261 gastric cancer patients who underwent LTG, D2 lymphadenectomy, and Roux-en-Y EJS with complete postoperative 6-month follow-up data at the General Surgery Department of Nanfang Hospital from October 2018 to June 2021 were collected. Among these 261 patients, 139 underwent EJS with a circular stapler via mini-laparotomy (extracorporeal group), while 122 underwent intracorporeal EJS (intracorporeal group), including 43 with OrVil(TM) anastomosis (OrVil(TM) subgroup) and 79 with Overlap anastomosis (Overlap subgroup). Compared with the extracorporeal group, the intracorporeal group had higher body mass index, smaller tumor size, earlier T stage and M stage (all P<0.05). Compared with the Overlap subgroup, the Orvil(TM) subgroup had higher proportions of upper gastrointestinal obstruction and esophagus involvement, and more advanced T stage (all P<0.05). No other significant differences in the baseline data were found (all P>0.05). The primary outcome was complications at postoperative 6-month. The secondary outcomes were operative status, intraoperative complication and postoperative recovery. Continuous variables with a skewed distribution are expressed as the median (interquartile range), and were compared using Mann-Whitney U test. Categorical variables are expressed as the number and percentage and were compared with the Pearson chi-square, continuity correction or Fisher's exact test. Results: Compared with the extracorporeal group, the intracorporeal group had smaller incision [5.0 (1.0) cm vs. 8.0 (1.0) cm, Z=-10.931, P=0.001], lower rate of combined organ resection [0.8% (1/122) vs. 7.9% (11/139), χ(2)=7.454, P=0.006] and higher rate of R0 resection [94.3% (115/122) vs. 84.9 (118/139), χ(2)=5.957, P=0.015]. The morbidity of intraoperative complication in the extracorporeal group and intracorporeal group was 2.9% (4/139) and 4.1% (5/122), respectively (χ(2)=0.040, P=0.842). In terms of postoperative recovery, the extracorporeal group had shorter time to liquid diet [(5.1±2.4) days vs. (5.9±3.6) days, t=-2.268, P=0.024] and soft diet [(7.3±3.7) days vs. (8.8±6.5) days, t=-2.227, P=0.027], and shorter postoperative hospital stay [(10.5±5.1) days vs. (12.2±7.7) days, t=-2.108, P=0.036]. The morbidity of postoperative complication within 6 months in the extracorporeal group and intracorporeal group was 25.9% (36/139) and 31.1%, (38/122) respectively (P=0.348). Furthermore, there was also no significant difference in the morbidity of postoperative EJS complications [extracorporeal group vs. intracorporeal group: 5.0% (7/139) vs. 82.% (10/122), P=0.302]. The severity of postoperative complications between the two groups was not statistically significant (P=0.289). In the intracorporeal group, the Orvil(TM) subgroup had more estimated blood loss [100.0 (100.0) ml vs.50.0 (50.0) ml, Z=-2.992, P=0.003] and larger incision [6.0 (1.0) cm vs. 5.0 (1.0) cm, Z=-3.428, P=0.001] than the Overlap subgroup, seemed to have higher morbidity of intraoperative complication [7.0% (3/43) vs. 2.5% (2/79),P=0.480] and postoperative complications [37.2% (16/43) vs. 27.8% (22/79), P=0.286], and more severe classification of complication (P=0.289). Conclusions: The intracorporeal EJS after LTG has similar safety to extracorporeal EJS. As for intracorporeal EJS, the Overlap method is safer and has more potential advantages than Orvil(TM) method, and is worthy of further exploration and optimization.

Two Randomized Phase 3 Studies of Aducanumab in Early Alzheimer's Disease

BACKGROUND

Alzheimer's disease is a progressive, irreversible, and fatal disease for which accumulation of amyloid beta is thought to play a key role in pathogenesis. Aducanumab is a human monoclonal antibody directed against aggregated soluble and insoluble forms of amyloid beta.

OBJECTIVES

We evaluated the efficacy and safety of aducanumab in early Alzheimer's disease.

DESIGN

EMERGE and ENGAGE were two randomized, double-blind, placebo-controlled, global, phase 3 studies of aducanumab in patients with early Alzheimer's disease.

SETTING

These studies involved 348 sites in 20 countries.

PARTICIPANTS

Participants included 1638 (EMERGE) and 1647 (ENGAGE) patients (aged 50-85 years, confirmed amyloid pathology) who met clinical criteria for mild cognitive impairment due to Alzheimer's disease or mild Alzheimer's disease dementia, of which 1812 (55.2%) completed the study.

INTERVENTION

Participants were randomly assigned 1:1:1 to receive aducanumab low dose (3 or 6 mg/kg target dose), high dose (10 mg/kg target dose), or placebo via IV infusion once every 4 weeks over 76 weeks.

MEASUREMENTS

The primary outcome measure was change from baseline to week 78 on the Clinical Dementia Rating Sum of Boxes (CDR-SB), an integrated scale that assesses both function and cognition. Other measures included safety assessments; secondary and tertiary clinical outcomes that assessed cognition, function, and behavior; and biomarker endpoints.

RESULTS

EMERGE and ENGAGE were halted based on futility analysis of data pooled from the first approximately 50% of enrolled patients; subsequent efficacy analyses included data from a larger data set collected up to futility declaration and followed prespecified statistical analyses. The primary endpoint was met in EMERGE (difference of -0.39 for high-dose aducanumab vs placebo [95% CI, -0.69 to -0.09; P=.012; 22% decrease]) but not in ENGAGE (difference of 0.03, [95% CI, -0.26 to 0.33; P=.833; 2% increase]). Results of biomarker substudies confirmed target engagement and dose-dependent reduction in markers of Alzheimer's disease pathophysiology. The most common adverse event was amyloid-related imaging abnormalities-edema.

CONCLUSIONS

Data from EMERGE demonstrated a statistically significant change across all four primary and secondary clinical endpoints. ENGAGE did not meet its primary or secondary endpoints. A dose- and time-dependent reduction in pathophysiological markers of Alzheimer's disease was observed in both trials.

Effects of wearing personal protective equipment during COVID-19 pandemic on composition and diversity of skin bacteria and fungi of medical workers

BACKGROUND

During the COVID-19 pandemic, wearing PPE can induce skin damage such as erythema, pruritus, erosion, and ulceration among others. Although the skin microbiome is considered important for skin health, the change of the skin microbiome after wearing PPE remain unknown.

OBJECTIVE

The present study aimed to characterize the diversity and structure of bacterial and fungal flora on skin surfaces of healthcare workers wearing personal protective equipment (PPE) during the COVID-19 pandemic using metagenomic next-generation sequencing (mNGS).

METHODS

A total of 10 Chinese volunteers were recruited and the microbiome of their face, hand, and back were analyzed before and after wearing PPE. Moreover, VISIA was used to analyze skin features.

RESULTS

Results of alpha bacterial diversity showed that there was statistically significant decrease in alpha diversity indice in the skin samples from face, hand, and three sites after wearing PPE as compared with the indice in the skin samples before wearing PPE. Further, the results of evaluated alpha fungal diversity show that there was a statistically significant decrease in alpha diversity indices in the skin samples from hand after wearing PPE as compared with the indices in the skin samples before wearing PPE (P<0.05). Results of the current study found that the main bacteria on the face, hand, and back skin samples before wearing the PPE were Propionibacterium spp. (34.04%), Corynebacterium spp. (13.12%), and Staphylococcus spp. (38.07%). The main bacteria found on the skin samples after wearing the PPE were Staphylococcus spp. (31.23%), Xanthomonas spp. (26.21%), and Cutibacterium spp. (42.59%). The fungal community composition was similar in three skin sites before and after wearing PPE.

CONCLUSION

It was evident that wearing PPE may affect the skin microbiota, especially bacteria. Therefore, it was evident that the symbiotic microbiota may reflect the skin health of medical workers during the COVID-19 pandemic.

Correlation of polyp grading scales with patient symptom scores and olfaction in chronic rhinosinusitis: a systematic review and meta-analysis

BACKGROUND

Various nasal polyp (NP) scoring systems have been proposed and used in the literature. However, no single system has been identified as superior. Correlations between NP scoring systems and patient symptoms, quality of life (QOL) or olfaction vary widely.

METHODS

A systematic search of PubMed, CINAHL, Scopus, and Cochrane Library was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-analyses guideline. Any study examining endoscopy scores and symptom, QOL or olfaction measures in cross sectional manner or after therapeutic intervention were included.

RESULTS

This review identified 55 studies for a pooled meta-analysis of Lund-Kennedy (LK-NP) polyp scores (N = 6), Meltzer scores (N = 6), Nasal polyp scores (NPS; N = 19), Total polyp score (TPS; N=8) Lilholdt scores (N = 8), Olfactory cleft endoscopy score (OCES; N =4), Discharge, inflammation, polyp/edema score (DIP; N = 2), and Perioperative sinus endoscopy score (POSE; N = 2). Meta-regression assessed correlations between NP grading systems and SNOT-22, nasal congestion scores, total nasal symptom scores (TNSS), and Smell Identification Test-40 (SIT40). None of the NP grading systems correlated significantly with any symptom, QOL or olfactory metric. In intervention studies of surgery or monoclonal antibody treatment, changes in NPS scores did not correlate with any patient reported outcome measure (PROM) or olfactory outcomes.

CONCLUSION

Current NP endoscopic scoring systems are not associated with PROMs such as SNOT-22, nasal congestion scores, and TNSS as well as objective measures of olfaction. NP grading systems with improved clinical utility are needed.

[The function of auditory cortex in the elderly using functional near-infrared spectroscopy technology]

Objective: Functional near-infrared spectroscopy (fNIRS) was used to study the effect of aging on the neuroimaging characteristics of cerebral cortex in the process of speech perception. Method: Thirty-four adults with normal hearing were recruited from March 2021 to June 2021, including 17 in the young group, with 6 males, 11 females, age (32.1±5.0) years, age range 20-39 years. and 17 in the elderly group, with 6 males, 11 females, age (63.2±2.8) years, age range 60-70 years. The test material was the sentence table of the Mandarin Hearing Test in Noise (MHINT). The task state block experiment design was adopted, and the temporal lobe, Broca's area, Wernicke's area, motor cortex were used as regions of interest. Objective brain imaging technology (fNIRS) combined with subjective psychophysical testing method was used to analyze the activation area and degree of cerebral cortex related to auditory speech perception in the elderly and young people under different listening conditions (quiet, signal-to-noise ratio of 10 dB, 5 dB, 0 dB, -5 dB). SPSS 23 software was used for statistical analysis. Result: The activation area and degree of activation in the elderly group were lower than those in the young group under each task condition; The number of activation channels in the young group were significantly more than those in the old group, and the number of activation channels in the left hemisphere were more than those in the right hemisphere, but there was no difference in the number of activation channels. There were more channels affected by age in the left hemisphere than in the right hemisphere. The activation degree of the young group when the signal-to-noise ratio was 0 dB was significantly higher than that of other signal-to-noise ratio conditions (P<0.05), but there was no significant difference in the old group under the five conditions (P>0.05). The speech recognition score of the young group was higher than that of the old group under all conditions. When the quiet and signal-to-noise ratio was 10 dB, the correct score of the two groups was equal or close to 100%. With the gradual decrease of signal-to-noise ratio, there was a significant difference between the two groups when the signal-to-noise ratio was 5 dB. The speech recognition accuracy of the young group decreased significantly when the signal-to-noise ratio was 0 dB, while that of the old group decreased significantly when the signal-to-noise ratio was 5 dB. Conclusions: With the increase of age, the speech perception in noisy environment and the activity of cerebral cortex gradually deteriorate, and the speech dominance hemisphere (left hemisphere) will be significantly affected by aging. The overall activation area and activation degree of the elderly under different speech tasks are lower than those of the young.

The association between 2,4-D and serum testosterone levels: NHANES 2013-2014

BACKGROUND

Previous studies have investigated associations between herbicides such as 2,4-Dichlorophenoxyacetic acid (2,4-D) and dyshormonogenesis, specifically low testosterone, in human, rodent, and cell models, but results have been conflicting and inconclusive.

METHODS

Using data from a cross-sectional study of 456 adult men in the 2013-2014 NHANES survey cycle, we examined the relationship between urinary concentrations of 2,4-D and serum testosterone levels.

RESULTS

Multivariable regression models adjusting for potential confounders revealed a significant, negative association between urinary 2,4-D and mean serum testosterone among U.S. adult males (β =  - 11.4 ng/dL, p = 0.02). Multivariable logistic regression models using a cutoff defining abnormally low testosterone (i.e., serum testosterone < 300 ng/dL) revealed no significant associations between 2,4-D and the odds of low testosterone.

CONCLUSION

These findings expand on previous literature implicating a role for 2,4-D in the etiology of low testosterone and dyshormonogenesis. Future studies are warranted to corroborate these findings, determine clinical significance, and to investigate the proposed potential biological mechanisms underlying this association.

Quantitative RNA assessment and long-term stability in the FFPE tumor samples using Digital Spatial Profiler

Background

Long-term storage of tissue slides has been reported to induce reduced biomarker (e.g. proteins and messenger RNA) detection. This study aimed to evaluate the impact of long-term storage time (0, 16, 24 and 36 weeks) and treatment conditions (non-paraffin and paraffin dipping) at 4°C on RNA quality in formalin-fixed and paraffin-embedded (FFPE) tissue sections.

Materials and methods

NanoString GeoMx Digital Spatial Profiling (DSP), a novel platform that allows spatial profiling, was used to profile RNA in human bladder cancer FFPE tissue sections.

Results

We observed excellent consistency of quantitative DSP RNA counts of all targets between two different treatment conditions (R > 0.97, Pearson correlation) at each time point and among all four different storage time points (R > 0.96, Pearson correlation) within each treatment condition. No significant difference was observed in the percentage of target genes with sufficient signal across two different treatment conditions at any time point (0 week, P = 0.96; 16 weeks, P = 0.76; 24 weeks, P = 0.96; 36 weeks, P = 0.76, Kolmogorov–Smirnov test) and across all four different storage time points (P > 0.05, Kolmogorov–Smirnov test) in either treatment condition.

Conclusion

Although both treatment conditions provided similar results in terms of count reproducibility and signal preservation, we recommend paraffin dipping to generate reproducible RNA results and optimize sample storage. Technology behind the NanoString GeoMx DSP platform shows a robust and reproducible RNA signal from multiple targets in the FFPE tissue sections stored at 4°C for at least up to 36 weeks.

•

Long-term storage of FFPE sections has been reported to induce reduced antigen detection especially for RNA.

•

This study evaluated the impact of storage times and treatment conditions on FFPE sections.

•

The GeoMx DSP system, a novel platform that allows spatial RNA profiling, has been utilized.

•

Long-term antigenicity preservation of quantitative DSP RNA counts was reported among storage times and treatment conditions.

•

This finding is valuable in low resourced settings where routine access to FFPE blocks is challenging.

SMDI: An Index for Measuring Subgingival Microbial Dysbiosis

An intuitive, clinically relevant index of microbial dysbiosis as a summary statistic of subgingival microbiome profiles is needed. Here, we describe a subgingival microbial dysbiosis index (SMDI) based on machine learning analysis of published periodontitis/health 16S microbiome data. The raw sequencing data, split into training and test sets, were quality filtered, taxonomically assigned to the species level, and centered log-ratio transformed. The training data set was subject to random forest analysis to identify discriminating species (DS) between periodontitis and health. DS lists, compiled by various "Gini" importance score cutoffs, were used to compute the SMDI for samples in the training and test data sets as the mean centered log-ratio abundance of periodontitis-associated species subtracted by that of health-associated ones. Diagnostic accuracy was assessed with receiver operating characteristic analysis. An SMDI based on 49 DS provided the highest accuracy with areas under the curve of 0.96 and 0.92 in the training and test data sets, respectively, and ranged from -6 (most normobiotic) to 5 (most dysbiotic) with a value around zero discriminating most of the periodontitis and healthy samples. The top periodontitis-associated DS were Treponema denticola, Mogibacterium timidum, Fretibacterium spp., and Tannerella forsythia, while Actinomyces naeslundii and Streptococcus sanguinis were the top health-associated DS. The index was highly reproducible by hypervariable region. Applying the index to additional test data sets in which nitrate had been used to modulate the microbiome demonstrated that nitrate has dysbiosis-lowering properties in vitro and in vivo. Finally, 3 genera (Treponema, Fretibacterium, and Actinomyces) were identified that could be used for calculation of a simplified SMDI with comparable accuracy. In conclusion, we have developed a nonbiased, reproducible, and easy-to-interpret index that can be used to identify patients/sites at risk of periodontitis, to assess the microbial response to treatment, and, importantly, as a quantitative tool in microbiome modulation studies.

[Proteinuria associated with hookworm infection: a case report]

As a common soil-borne nematode, hookworm is mainly parasitized in the intestine, and the clinical manifestations of hookworm infections mainly include gastrointestinal symptoms and iron-deficiency anemia. In addition, hookworm may be also parasitized in other organs in addition to gastrointestinal system, resulting in development of disorders in other systems. Proteinuria caused by hookworm infections is rare and easy to be misdiagnosed in clinical practices. Hereby, the diagnosis and treatment of a case of proteinuria associated with hookworm infections was reported, in order to increase the understanding of hookworm infection-associated proteinuria among clinicians.