In Situ Photo-Crosslinkable Protein Bioadhesive for Bone Graft Fixation

Bone grafting is a fundamental dental surgery procedure widely used for implant placement and periodontal disease management treatments. Despite its broad applications, vertical bone augmentation presents unique challenges, including the risk of graft displacement due to gravitational and masticatory forces. Traditional physical stabilization methods introduce additional complexities and risks, underscoring the need for innovative fixation technologies. This study aimed to develop an in situ photo-crosslinkable bioadhesive hydrogel (iPBAH) as a multifunctional bone graft binder to enhance the process of bone reconstruction. The bioadhesive is composed of mussel-derived adhesive protein (MAP) fused with the cell-adhesive peptide RGD. The numerous tyrosine residues in MAP facilitate rapid photo-crosslinking, enabling efficient hydrogel formation using visible blue light. Subsequently, iPBAH underwent comprehensive characterization to evaluate its suitability as a multifunctional bone graft binder. iPBAH efficiently underwent in situ crosslinking through harmless exposure to visible light within minutes and displayed several exceptional properties, including a microporous structure, underwater adhesion, extended durability, high compressive strength, and biocompatibility. In vivo assessments, using male Sprague-Dawley rats, demonstrated that iPBAH binder significantly enhanced bone regeneration in a rat calvarial bone defect model. The in situ crosslinking of the iPBAH binder during bone graft transplantation can effectively fill irregular and complex defect shapes while simultaneously preventing graft material leakage. The improved physical attributes of the bound graft material can enhance its resistance to external forces, thereby ensuring sustained retention over time. Moreover, the interaction between iPBAH and surrounding tissues promotes adhesion and integration of the graft material with host tissues in the defect area. In addition, the included RGD peptide in iPBAH can augment inherent cell recruitment, adhesion, and growth, consequently expediting osteogenesis.

Immature bovine cartilage wear is due to fatigue failure from repetitive compressive forces and not reciprocating frictional forces

OBJECTIVE

Wear of articular cartilage is not well understood. We hypothesize that cartilage wears due to fatigue failure in repetitive compression instead of reciprocating friction.

DESIGN

This study compares reciprocating sliding of immature bovine articular cartilage against glass in two testing configurations: (1) a stationary contact area configuration (SCA), which results in static compression, interstitial fluid depressurization, and increasing friction coefficient during reciprocating sliding, and (2) a migrating contact area configuration (MCA), which maintains pressurization and low friction while producing repetitive compressive loading in addition to reciprocating sliding. Contact pressure, sliding duration, and sliding distance were controlled to be similar between test groups.

RESULTS

SCA tests exhibited an average friction coefficient of μ=0.084±0.032, while MCA tests exhibited a lower average friction coefficient of μ=0.020±0.008 (p<10-4). Despite the lower friction, MCA cartilage samples exhibited clear surface damage with a significantly greater average surface deviation from a fitted plane after wear testing (Rq=0.125±0.095 mm) than cartilage samples slid in a SCA configuration (Rq=0.044±0.017 mm, p=0.002), which showed minimal signs of wear. Polarized light microscopy confirmed that delamination damage occurred between the superficial and middle zones of the articular cartilage in MCA samples.

CONCLUSIONS

The greatest wear was observed in the group with lowest friction coefficient, subjected to cyclical instead of static compression, implying that friction is not the primary driver of cartilage wear. Delamination between superficial and middle zones implies the main mode of wear is fatigue failure under cyclical compression, not fatigue or abrasion due to reciprocating frictional sliding.

Significance of Radiomics in Predicting Local Control for Patients with Malignant Liver Tumors Treated Using Stereotactic Body Radiotherapy

PURPOSE/OBJECTIVE(S)

We routinely deliver Stereotactic Body Radiotherapy (SBRT) in malignant liver tumors using planning computed tomography (CT) and Magnetic Resonance Images (MRI) to aid target definition. In this study, we extracted radiomic features from the MR images to predict local control (LC) post-SBRT.

MATERIALS/METHODS

We retrospectively analyzed patients with either hepatocellular cancers (HCCs) or liver metastases (Mets) treated with SBRT between Aug 2014 and Aug 2020. All patients had CT simulation followed by 1.5 Tesla planning MRI in treatment position. Contrast enhanced T1 VIBE and T2 Haste MR sequences were registered with planning CT for target definition. Radiomic features were extracted from Gross Tumor Volumes (GTV) masked out of 60 seconds post contrast T1 VIBE MR images using the Radiomics calculator tool RaCaT. The output included 480 (408 textural, 50 intensity and 22 morphological) features for each target. Principal Component Analysis of the outputs obtained from all the targets yielded 20 radiomic feature clusters after computational prioritization. These clusters were correlated to LC outcomes at various time points post-SBRT. LC was defined as non-progressive disease. Accuracy of predictions was measured by area under (AUC) receiver operating characteristic curve. Cox regression analysis was done to find univariate and multivariate clinical [HCCs vs. Mets, single vs. multiple lesions, previous local therapy (yes vs. no), GTV volume (≤40 vs. >40 cc)], radiomic and dosimetric predictors (continuous) of LC.

RESULTS

In total, 97 patients received SBRT to 122 lesions. The median dose prescribed was 45 Gy (range, 30-50 Gy). Median age was 69 years (interquartile range, IQR 61-73 yrs.). 59 patients had HCCs and 38 had Mets. 24 lesions had prior ablative therapy. 75 patients had one target, and 22 had multiple targets. Median GTV was 43.5 cc (IQR 23.4-78.6 cc). Median follow up was 16.6 months (IQR 9.7-27.2 mths). Median LC was 13.6 months (IQR 8.0-23.5 mths). On univariate analysis, histology (HCCs vs. Mets; Hazard ratio (HR) 2.9, 95% CI 1.4-6.4; p < 0.006), radiomic clusters (p < 0.006) and the max., mean, and min. doses to GTV and Planning Target Volumes correlated with improved LC (all p-values < 0.05). On multivariate analysis, histology (HCCs vs. Mets; HR 4.4, 95% CI 1.6-12.3; p = 0.004), radiomic clusters (p = 0.034) and prescription dose (p = 0.048) were significant covariates. Specifically, the 20 radiomic clusters were predictive of LC, and the accuracy of predictions showed promise with AUC values of 0.74, 0.80, and 0.81 at 12, 24, and 36 months post-SBRT, respectively. AUC values for LC in HCCs vs. Mets at 12, 24, and 36 months were 0.83, 0.77, and 0.70, and 0.66, 0.77, and 0.88, respectively.

CONCLUSION

MR-based radiomics predict LC post-SBRT in patients with malignant liver tumors. Further research focused on independent validation of the model is required to explore its clinical use.

Niche and ecosystem preference of earliest diverging fungi in soils

Within the supergroup Rotosphaeromycetes, or "Holomycota"/"Nucletmycea", there are several well-recognised unicellular clades in the earliest diverging fungi (EDF). However, we know little about their occurrence. Here, we investigated EDF in the rhizosphere and bulk soils from cropland, forest, orchard, and wetland ecosystems around the Beijing-Hebei area, China, to illustrate their niche and ecosystem preference. More than 500 new operational taxonomic units (OTUs) of EDF were detected based on the 18S rRNA genes. Microsporida and Aphelida constitute dominant groups, whereas Rozellosporida was quite rare. Although the EDF community was site-specific, the soil chemical characteristics, vegetation, and other eukaryotic microorganisms were the key factors driving the occurrence of EDF. Moreover, the stochastic process consisted the most of the EDF community assembly.

Deep Learning of Time-Signal Intensity Curves from Dynamic Susceptibility Contrast Imaging Enables Tissue Labeling and Prediction of Survival in Glioblastoma

BACKGROUND AND PURPOSE

An autoencoder can learn representative time-signal intensity patterns to provide tissue heterogeneity measures using dynamic susceptibility contrast MR imaging. The aim of this study was to investigate whether such an autoencoder-based pattern analysis could provide interpretable tissue labeling and prognostic value in isocitrate dehydrogenase (IDH) wild-type glioblastoma.

MATERIALS AND METHODS

Preoperative dynamic susceptibility contrast MR images were obtained from 272 patients with IDH wild-type glioblastoma (training and validation, 183 and 89 patients, respectively). The autoencoder was applied to the dynamic susceptibility contrast MR imaging time-signal intensity curves of tumor and peritumoral areas. Representative perfusion patterns were defined by voxelwise K-means clustering using autoencoder latent features. Perfusion patterns were labeled by comparing parameters with anatomic reference tissues for baseline, signal drop, and percentage recovery. In the validation set (n = 89), a survival model was created from representative patterns and clinical predictors using Cox proportional hazard regression analysis, and its performance was calculated using the Harrell C-index.

RESULTS

Eighty-nine patients were enrolled. Five representative perfusion patterns were used to characterize tissues as high angiogenic tumor, low angiogenic/cellular tumor, perinecrotic lesion, infiltrated edema, and vasogenic edema. Of these, the low angiogenic/cellular tumor (hazard ratio, 2.18; P = .047) and infiltrated edema patterns (hazard ratio, 1.88; P = .009) in peritumoral areas showed significant prognostic value. The combined perfusion patterns and clinical predictors (C-index, 0.72) improved prognostication when added to clinical predictors (C-index, 0.55).

CONCLUSIONS

The autoencoder perfusion pattern analysis enabled tissue characterization of peritumoral areas, providing heterogeneity and dynamic information that may provide useful prognostic information in IDH wild-type glioblastoma.

[The status and influencing factors of presenteeism among clinical nurses: a systematic review]

Objective: To systematically review the status and factors influencing presenteeism among clinical nurses. Methods: In December 2021, CNKI, CBM, Wanfang, VIP, Web of Science, PubMed, Embase, The Cochrane Library, CINAHL, PsyclNFO and other databases were electronically searched to cross sectional studies on the current situation and factors influencing the occurrence of presenteeism among clinical nurses. The search terms mainly included presenteeism, sick at work, Stanford Presenteeism Scale, nurse, level, risk factor, influence, et al. And the search time was from the establishment of the database to November 30, 2021. Literature screening, data extraction and evaluation of the risk of bias in the included literature were done independently by two researchers, and meta-analysis was performed using Stata 15.1 software. Results: A total of 29 studies involving 13 535 clinical nurses were included.The results of the meta-analysis showed that the score of presenteeism was 17.99 [95% CI (17.02-18.95), P =0.000]. Subgroup analysis showed that presenteeism scores were higher in articles published before 2020 (ES=19.28, 95%CI: 18.41-20.15, P=0.000) and in the group of nurses aged 36 to 40 years (ES=19.27, 95%CI: 17.35~21.19, P=0.000), female (ES= 17.04, 95%CI: 14.70-19.39, P=0.000), secondary school education (ES=21.01, 95%CI: 17.76-24.26, P= 0.007), married (ES=17.49, 95%CI: 15.13-19.85, P=0.000), working for 5 to 10 years (ES=17.78, 95%CI: 16.54-19.02, P=0.000), contract (ES=17.05, 95%CI: 15.23-18.87, P=0.000), working in pediatrics (ES= 16.65, 95% CI: 15.31-17.99, P=0.000) and European region (ES =21.21, 95% CI: 20.50-21.93, P=0.000) . Conclusion: Current evidence suggests that clinical nurses are at high risk of presenteeism, which is affected by variety of factors. The managers should pay attention to the physical and mental health of nurses, identify high-risk factors as early as possible and take measures to reduce the occurrence of presenteeism and improve the quality of nursing.

Incidence and predictors of transthyretin cardiac amyloidosis in patients with degenerative aortic stenosis

Background

The approval of new therapies for treating transthyretin (TTR) cardiac amyloidosis has led to significant interest in identifying patients at high risk for this disease. Investigators have identified a correlation between severe degenerative aortic stenosis (AS) and TTR cardiac amyloidosis in older patients, with several studies finding up to 20% of patients who undergo transcatheter aortic valve replacement (TAVR) having TTR cardiac amyloidosis. These initial TAVR studies were conducted when TAVR was performed almost exclusively in high surgical risk populations. Therefore, the true incidence of TTR cardiac amyloidosis in an all-comers with severe degenerative AS referred for TAVR is unknown.

Purpose

To identify the true burden of TTR cardiac amyloidosis in a contemporary population of severe degenerative AS undergoing TAVR screening.

Methods

All patients ≥70 years with severe native valve degenerative AS seen in a multidisciplinary valve clinic were referred for technetium-99m pyrophosphate cardiac scintigraphy (PYP scan) for evaluation of cardiac amyloidosis. Diagnosis was made via combination of planar grade and heart to contralateral lung ratio, confirmed on single positron emission computed tomography/computed tomography (SPECT/CT). Patients with a positive PYP scan were referred to a heart failure clinic where they underwent testing for AL amyloidosis.

Results

Over a 10 month period, 247 patients seen in valve clinic underwent a PYP scan. Of this cohort, 203 patients ultimately underwent TAVR, 15 surgical aortic valve replacement, and 2 balloon valvuloplasty with 27 patients having not yet undergone a procedure. The positivity rate was 4% (10/247) with 1 patient having an equivocal result. The patients with a positive PYP scan had higher rate of low-flow low-gradient (LFLG) AS (64% vs 29%, p=0.006) and classical LFLG AS (27% vs 8%, p=0.02). Echocardiographic measures associated with a positive PYP scan include a lower global longitudinal strain (−10.0% vs −16.1%, p=0.008), lower average e' (4.5 vs 6.5, p=0.003), and an increased E/A ratio (1.8 vs 1.1, p=0.018).

Conclusions

The incidence of TTR amyloidosis in a contemporary, severe AS population ≥70 years undergoing TAVR screening appears much lower than previously described in the literature. Echocardiographic traits may be able to predict which patients with severe AS should undergo evaluation for TTR cardiac amyloidosis.

Funding Acknowledgement

Type of funding sources: None.

Distinctive microbiota distribution from healthy oral to post-treatment apical periodontitis

Post-treatment apical periodontitis (PoAP) occurs when root canal treatment has not adequately eliminated bacterial invasion and infection. Yet little is known about the bacterial composition and changes related to the etiology and pathogenesis of PoAP. In this study, clinical samples classified as root apex (HARD) and periapical granulation tissues (SOFT) were separately collected from 10 patients with PoAP. The microbiota of each sample was characterized by 16S rRNA gene sequencing, and the obtained dataset was coanalyzed with 20 NCBI sequence read archive (SRA) datasets of healthy oral (HO) and primary apical periodontitis (PAP). We observed 2522 operational taxonomic units (OTUs) belonging to 29 phyla, and all samples shared 86.5% of the sequence reads. The OTUs affiliated with Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria, and Actinobacteria, were identified as core microbiota, which accounted for nearly 90% of 16S rRNA sequences in all samples. However, the principal coordinates analysis (PCoA) of the beta diversity demonstrated that the three periapical statuses have distinct microbial compositions. Compared with HO and PoAP, Actinomyces has a significantly increased abundance in PAP. The microbial diversities in PoAP were significantly lower than those in the HO and PAP (p&lt;0.05). The relative abundance of most bacterial taxa was decreasing, except that Clostridia and Synergistia were increased. Furthermore, we explored the potential metabolic differences of the microbial communities by KEGG pathway prediction. We revealed that the microbiota of PoAP might have a more active metabolic capacity, including carbohydrate metabolism, energy metabolism, and enzyme cofactor/carrier biosynthesis (p&lt;0.05). Our study revealed that invasion of opportunistic pathogens such as Clostridia and Synergistia might play a significant role in PoAP, thus guiding the further study of complex microbial-host interactions and the development of more effective diagnostic and therapeutic methods.

Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction

Although the study of aerobic methane-oxidizing bacteria (MOB, methanotrophs) has been carried out for more than a hundred years, there are many uncultivated methanotrophic lineages whose metabolism is largely unknown. Here, we reconstructed a nearly complete genome of a Beijerinckiaceae methanotroph from the enrichment of paddy soil by using nitrogen-free M2 medium. The methanotroph labeled as MO3_YZ.1 had a size of 3.83 Mb, GC content of 65.6%, and 3442 gene-coding regions. Based on phylogeny of pmoA gene and genome and the genomic average nucleotide identity, we confirmed its affiliation to the MO3 lineage and a close relationship to Methylocapsa. MO3_YZ.1 contained mxaF- and xoxF-type methanol dehydrogenase. MO3_YZ.1 used the serine cycle to assimilate carbon and regenerated glyoxylate through the glyoxylate shunt as it contained isocitrate lyase and complete tricarboxylic acid cycle-coding genes. The ethylmalonyl-CoA pathway and Calvin–Benson–Bassham cycle were incomplete in MO3_YZ.1. Three acetate utilization enzyme-coding genes were identified, suggesting its potential ability to utilize acetate. The presence of genes for N₂ fixation, sulfur transformation, and poly-β-hydroxybutyrate synthesis enable its survival in heterogeneous habitats with fluctuating supplies of carbon, nitrogen, and sulfur.

Impact of doppler velocity index after transcatheter aortic valve replacement using Sapien-3 valve – a single centre experience

Background

Little is known about the hemodynamic performance of Edwards Sapien-3 (S3) valve after Transcatheter Aortic Valve Replacement (TAVR). Doppler velocity index (DVI) is a better indicator of prosthetic valve function as it is independent of valve size and flow, unlike mean gradient and peak velocity which are flow-dependent.

Methods

In this study, we compare outcomes based on differences in DVI among a consecutive series of patients who underwent S3 TAVR between April 2015 and December 2018. Our institutional review board approved the study and informed consents were obtained from the subjects.

Results

Among 921 patients who had follow-up echocardiograms within 30 days after TAVR, 60.8% had DVI ≤0.5, while 39.2% had DVI &gt;0.5. The median 30-day DVI was 0.47 with a standard deviation of 0.11 and mean 0.49 and interquartile range 0.41–0.55. The baseline clinical and procedural characteristics were similar between both groups with the exception of less post-dilation (36.8% vs. 47.4%; p=0.001) and greater implantation depth (2.59±1.99 vs. 2.31±1.9mm; p=0.031) with DVI ≤0.5. The rates of aortic valve calcification, pre dilation, pre-TAVR aortic regurgitation (AR) were similar. At baseline, there were no differences between both groups in mean or peak gradients or aortic velocity time integral (VTI). At 1 year, mean gradients were higher with DVI ≤0.5 (12.7±5.6 vs. 11.1±4.6 mmHg; p=0.001). DVI ≤0.5 was associated with higher peak gradients (24.2±10.2 vs. 21.4±8.7 mmHg; p=0.002), and aortic VTI (51.4±13.5 vs. 46.8±12.2 cm; p&lt;0.001) at 1 year, especially with the 26mm and 29mm prostheses. Compared with DVI&gt;0.5 group, patients in DVI&lt;0.5 group had lower baseline left ventricular ejection fraction (LVEF) (54.5±12.2% vs. 58.9±11.2%; p&lt;0.001), higher left ventricular end-diastolic volume index (LVEDVi) (54.3±20.9 vs. 49.4±17.4 ml/m2; p=0.001), higher LV end-systolic volume index (LVESVi) (25.2±16.5 vs. 21.3±12.7 ml/m2; p=0.001), and similar LV mass index (110.7±31.9 vs. 106.9±32.7 g/m2; p=0.134). 1-year mortality rates among patients who had DVI ≤0.5 compared to DVI &gt;0.5 were lower (6.6% vs. 10.6%; log-rank p=0.033), however no difference was noted at both 2 years (17.3% vs. 20.1%; log-rank p=0.151), and 3 years after TAVR (30.7% vs. 31.2%; log-rank p=0.333).

Conclusions

DVI&lt;0.5 was associated with higher peak gradients and lower baseline LVEF. DVI &lt;0.5 group patients had lower 1-year mortality but similar mortality at 2 and 3-years of follow up.

Funding Acknowledgement

Type of funding sources: None. Figure 1. All-cause SurvivalFigure 2. Hemodynamic Data

Late Clinical and Hemodynamic Outcomes in patients with degenerated bioprosthetic aortic valves undergoing transcatheter valve-in-valve implantation

Background

Clinical studies have shown promising early outcomes for valve-in-valve transcatheter aortic valve implantation (ViV-TAVI); however, the late outcomes of this procedure remain under-investigated.

Purpose

We performed the present analysis to assess the late clinical and hemodynamic outcomes of ViV-TAVI in patients with degenerated bioprosthetic aortic valves.

Methods

A comprehensive chart review was performed for eligible patients to retrieve data on procedural characteristics, admission details following the procedure, and echocardiographic parameters. Clinical outcomes included all-cause mortality, heart failure hospitalization and structural valve deterioration (SVD), as defined by VARC-II criteria, up to 5 years of follow-up. To assess the trends in mean and peak transvalvular gradients, data from the follow-up echocardiographic reports were analyzed using Syngo Dynamics imaging software.

Results

A total of 188 patients were included with a mean age of 75.8±10.4 years. Balloon- and self-expandable valves were used in 155 (82.4%) and 33 (17.6%) patients, respectively. At 30 days, 3 (1.6%) patients died and 8 (4.2%) required hospitalization for heart failure, while at 5 years, both events were recorded in 29 (15.4%) and 37 (19.7) patients, respectively. Kaplan-Meier survival analysis showed that patients with smaller surgical valves (internal diameter ≤21 mm) had a significantly higher mortality rate (log-rank p=0.021) than those with larger valves; however, no significant difference (log-rank p=0.59) was detected between different transcatheter valves (self vs. balloon-expandable). Three patients underwent re-intervention, performed via a transcatheter approach. Further, assessment of follow-up echocardiographic reports revealed 9 (4.8%) cases of SVD, as well as stable mean (16.3±6.9 at discharge and 16.9±11.3) and peak (30.3±12.1 at discharge and 30.7±18.4 at 5 years) transvalvular gradients. No difference (p&gt;0.05) was observed based on transcatheter valve type or surgical valve internal diameter in terms of mean and peak transvalvular gradients throughout the follow-up period.

Conclusion

The present study showed good clinical outcomes among patients undergoing VIV-TAVI, with stable VIV performance over a five-year period. Future long-term studies are warranted to analyze the predictors of outcomes following ViV-TAVI and explore the role of this treatment option in the life-long management of aortic stenosis.

Funding Acknowledgement

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): Jennifer and Robert McNeil Donation to the Heart, Thoracic, and Vascular Institute at Cleveland Clinic. Figure 1

Outcomes of transfemoral-transcatheter aortic valve replacement with Sapien-3 valve in liver cirrhosis patients

Background

Little is known about the outcomes of liver cirrhosis patients with severe aortic stenosis (AS) who undergo transcatheter aortic valve replacement (TAVR).

Methods

We undertook a retrospective analysis of consecutive patients with severe symptomatic AS who underwent transfemoral-TAVR with Sapien-3 valve at our Clinic between April 2015 and December 2018, yielding 32 patients with liver cirrhosis on imaging including ultrasound and/or computed tomography. Their baseline characteristics, procedural and long-term outcomes after TAVR with the non-cirrhotic group were compared, along with their management strategies as per the hepatology team.

Results

Among 1028 patients, 32 were assigned to the cirrhosis, and 996 were assigned to the non-cirrhosis (control) group. Compared with the control group cirrhotic patients were slightly younger in age (74.5 vs 81.2 years), had a slightly higher BMI (31.3 vs 29.3), and had a higher incidence of prior history of myocardial infarction (38% vs 33%). Baseline variables including the history of smoking, hypertension, diabetes, and atrial fibrillation were comparable in both groups. Among cirrhotic patients (n=32), the most common etiologies were non-alcoholic steatohepatitis (NASH) (37.5%), Alcoholism (18.75%), and Hepatitis C (12.5%). The mean MELD-NA score was 11.8 and 67% of patients were Child PUGH Class A and 33% were Child PUGH Class B and all patients had a Child PUGH score of ≥5. 53% of patients (n=17) in the cirrhosis group were evaluated by Hepatology and 12.5% (n=4) were evaluated for a liver transplant but only 1 patient had a liver transplant post-TAVR. Compared with the control group cirrhotic patients had similar 1-year mortality (12% vs 12%, p=1), had a lower rate of 30-day new pacemaker post tavr (6% vs 9% p=0.85), had a higher rate of 1-year readmission for heart failure (12% vs 5% p=0.12) and similar 1-year major adverse cardiac and cerebrovascular event (MACCE) rate (15% vs 14% p=0.98)

Conclusion

Patients with severe AS undergoing TAVR with concomitant liver cirrhosis demonstrate comparable outcomes compared with their non- cirrhotic counterparts. NASH followed by alcoholic cirrhosis was found to be most common etiology.

Funding Acknowledgement

Type of funding sources: None. Figure 1Figure 2

Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau

The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using ¹³ C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H₄ MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.

Comparison of uniaxial and triaxial accelerometer outputs among individuals with and without Down syndrome

BACKGROUND

Using uniaxial accelerometry approach in measuring physical activity levels of individuals with Down syndrome (DS) might underestimate their energy expenditure due to the unique mediolateral walking pattern. Therefore, the purpose of this study was to examine and compare the relationship between two types of accelerometer outputs, uniaxial and triaxial, and energy expenditure in individuals with and without DS.

METHODS

Eighteen participants with DS and 19 participants without DS wore a GT3X+ accelerometer and a portable metabolic system in three different walking conditions.

RESULTS

Correlations between V̇O2 and each of the two accelerometer outputs (uniaxial: r = 0.75, triaxial: r = 0.75) were not significantly different among individuals without DS (z = 0.14, P = 0.89); however, significant differences in the relationship between V̇O2 and accelerometer outputs (uniaxial: r = 0.53, triaxial: r = 0.64) were observed among individuals with DS (z = -1.72, P < 0.046).

CONCLUSIONS

The findings suggest that when using accelerometers to measure physical activity levels for individuals with DS, triaxial outputs may better predict physical activity levels.

Interfacial Nanoinjection-Based Nanoliter Single-Cell Analysis

Single-cell analysis offers unprecedented resolution for the investigation of cellular heterogeneity and the capture of rare cells from large populations. Here, described is a simple method named interfacial nanoinjection (INJ), which can miniaturize various single-cell assays to be performed in nanoliter water-in-oil droplets on standard microwell plates. The INJ droplet handler can adjust droplet volumes for multistep reactions on demand with high precision and excellent monodispersity, and consequently enables a wide range of single-cell assays. Importantly, INJ can be coupled with fluorescence-activated cell sorting (FACS), which is currently the most effective and accurate single-cell sorting and isolation method. FACS-INJ pipelines for high-throughput plate well-based single-cell analyses, including single-cell proliferation, drug-resistance testing, polymerase chain reaction (PCR), reverse-transcription PCR, and whole-genome sequencing are introduced. This FACS-INJ pipeline is compatible with a wide range of samples and can be extended to various single-cell analysis applications in microbiology, cell biology, and biomedical diagnostics.

High-throughput single-cell cultivation reveals the underexplored rare biosphere in deep-sea sediments along the Southwest Indian Ridge

Microorganisms in the deep sea play vital roles in marine ecosystems. However, despite great advances brought by high throughput sequencing and metagenomics, only a small portion of microorganisms living in the environment can be cultivated in the laboratory and systematically studied. In this study, an improved high-throughput microfluidic streak plate (MSP) platform was developed to speed up the isolation of microorganisms from deep-sea sediments and evaluated with deep-sea sediments collected from the Southwest Indian Ridge (SWIR). Based on our previously reported MSP method, we improved its isolation efficiency with a semi-automated droplet picker and improved humidity control to enable long-term cultivation with a low-nutrient medium for up to five months according to the slow-growing nature of most deep-sea species. The improved MSP method allows the isolation of microbes by selection and investigation of microbial diversity by high throughput sequencing of the pooled sample cultures. By picking individual droplets and scale-up cultivation, a total of 772 strains that were taxonomically assigned to 70 species were isolated from the deep-sea sediments in the SWIR, including 15 potential novel species. On the other hand, based on 16S rRNA gene amplicon sequencing analysis, the microbial diversity of the SWIR was studied and documented with culture-dependent and independent methods in this study. The superiority of the MSP platform in revealing the rare biosphere was also evaluated based on amplicon sequencing. The results show that droplet-based single-cell cultivation of the MSP has a much higher ability than traditional agar plate cultivation in obtaining microbial species and more than 90% of operational taxonomic units (OTUs) detected in the MSP pool belong to the rare biosphere. Our results indicate the high robustness and efficiency of the improved MSP platform in revealing the environmentally rare biosphere, especially for slow-growing species. Overall, the MSP platform has a superior ability to recover microbial diversity than conventional agar plates and it was found to hold great potential for recovering rare microbial resources from various environments.

Full-scale anaerobic reactor samples would be more suitable than lab-scale anaerobic reactor and natural samples to inoculate the wheat straw batch anaerobic digesters

This study evaluated the effects of the inocula from natural wetland, lab-scale and full-scale anaerobic reactors on wheat straw anaerobic digestion. Three replicate batch reactors were constructed for each inoculum to investigate the reactor performances and microbial communities. Reactors seeded with full-scale reactor samples were started up most rapidly, achieved the highest methane production, and were recognized as the higher efficient reactors. The dominance of acetoclastic methanogens, including Methanosaeta and Methanoscrina, was crucial for the higher efficient reactors, whereas hydrogenotrophic methanogens were dominant in other reactors. Genus Treponema, which could enhance the cellulose degradation and conduct homoacetogenesis, was first reported to be dominant in the bacterial communities of high efficient reactors. Inoculum sources and process conditions were suggested to be the deterministic factors in shaping the microbial communities in the higher efficient reactors. These findings contribute to the startup of new anaerobic reactors.

Efficacy of dimethyl fumarate in Japanese multiple sclerosis patients: interim analysis of randomized, double-blind APEX study and its open-label extension

Background

Current data for the use of dimethyl fumarate (DMF) in Japanese patients with relapsing-remitting multiple sclerosis (RRMS) is limited.

Objectives

To assess the efficacy of DMF in Japanese patients with RRMS.

Methods

The phase 3, multinational APEX study (ClinicalTrials.gov identifier: NCT01838668) consisted of two parts: a 24-week double-blind part where subjects were randomized to receive DMF 240 mg or placebo twice daily in East Asian and Eastern European countries, and an open-label extension part where all subjects received DMF. The primary endpoint was the total number of new gadolinium-enhancing lesions in Weeks 12-24. In this interim analysis, we report efficacy data in the Japanese subgroup (DMF n = 56; placebo n = 58) over 72 weeks, including an extension phase.

Results

DMF reduced the total number of new gadolinium-enhancing lesions in Weeks 12-24 by 85% versus placebo (p < 0.0001). At Week 24, the annualized relapse rate was also reduced by 48% with DMF, versus placebo. DMF reduced the probability of relapse from Week 8 and was sustained. The number of gadolinium-enhancing lesions was maintained through 72 weeks.

Conclusions

DMF demonstrated sustained efficacy in this Japanese subgroup. The results were consistent with those observed in studies of DMF enrolling primarily Caucasian patients.

Upland Soil Cluster Gamma dominates methanotrophic communities in upland grassland soils

Aerobic methanotrophs in upland soils consume atmospheric methane, serving as a critical counterbalance to global warming; however, the biogeographic distribution patterns of their abundance and community composition are poorly understood, especial at a large scale. In this study, soils were sampled from 30 grasslands across >2000 km on the Qinghai-Tibetan Plateau to determine the distribution patterns of methanotrophs and their driving factors at a regional scale. Methanotroph abundance and community composition were analyzed using quantitative PCR and Illumina Miseq sequencing of pmoA genes, respectively. The pmoA gene copies ranged from 8.2 × 10⁵ to 1.1 × 10⁸ per gram dry soil. Among the 30 grassland soil samples, Upland Soil Cluster Gamma (USCγ) dominated the methanotroph communities in 26 samples. Jasper Ridge Cluster (JR3) was the most dominant methanotrophic cluster in two samples; while Methylocystis, cluster FWs, and Methylobacter were abundant in other two wet soil samples. Interestingly, reanalyzing the pmoA genes sequencing data from existing publications suggested that USCγ was also the main methanotrophic cluster in grassland soils in other regions, especially when their mean annual precipitation was <500 mm. Canonical Analysis of Principal Coordinates including all soil samples indicated that the methanotrophic community composition was significantly correlated with local environmental factors, among which mean annual precipitation and pH showed the strongest correlations. Variance partitioning analysis showed that environmental factors and spatial distance were significant factors affecting the community structure of methanotrophs, and environmental properties were more important factors. Collectively, these findings indicate that atmospheric methane may be mainly oxidized by USCγ in upland soils. They also highlight the key role of water availability and pH in determining the abundance and community profiles of grassland soil methanotrophs.

Methylococcaceae are the dominant active aerobic methanotrophs in a Chinese tidal marsh

Although coastal marshes are net carbon sinks, they are net methane sources. Aerobic methanotrophs in coastal marsh soils are important methane consumers, but their activity and populations are poorly characterized. DNA stable-isotope probing followed by sequencing was used to determine how active methanotrophic populations differed in the main habitats of a Chinese coastal marsh. These habitats included mudflat, native plant-dominated, and alien plant-dominated habitats. Methylococcaceae was the most active methanotroph family across four habitats. Abundant methylotroph sequences, including methanotrophs and non-methane-oxidizing methylotrophs (Methylotenera and Methylophaga), constituted 50-70% of the 16S rRNA genes detected in the labeled native plant-dominated and mudflat soils. Methylotrophs were less abundant (~ 20%) in labeled alien plant-dominated soil, suggesting less methane assimilation into the target community or a different extent of carbon cross-feeding. Canonical correspondence analysis indicated a significant correlation between the active bacterial communities and soil properties (salinity, organic carbon, total nitrogen, pH, and available phosphorus). Importantly, these results highlight how changing vegetation or soil features in coastal marshes may change their resident active methanotrophic populations, which will further influence methane cycling.

Dynamic Sessile-Droplet Habitats for Controllable Cultivation of Bacterial Biofilm

Bacterial biofilms play essential roles in biogeochemical cycling, degradation of environmental pollutants, infection diseases, and maintenance of host health. The lack of quantitative methods for growing and characterizing biofilms remains a major challenge in understanding biofilm development. In this study, a dynamic sessile-droplet habitat is introduced, a simple method which cultivates biofilms on micropatterns with diameters of tens to hundreds of micrometers in a microfluidic channel. Nanoliter plugs are utilized, spaced by immiscible carrier oil to initiate and support the growth of an array of biofilms, anchored on and spatially confined to the micropatterns arranged on the bottom surface of the microchannel, while planktonic or dispersal cells are flushed away by shear force of aqueous plugs. The performance of the aforementioned method of cultivating biofilms is demonstrated by Pseudomonas aeruginosa PAO1 and its derived mutants, and quantitative antimicrobial susceptibility testing of PAO1 biofilms. This method could significantly eliminate corner effects, avoid microchannel clogging, and constrain the growth of biofilms for long-term observations. The controllable sessile droplet-based biofilm cultivation presented in this study should shed light on more quantitative and long-term studies of biofilms, and open new avenues for investigation of biofilm attachment, growth, expansion, and eradication.

Morphine and pholcodine-specific IgE have limited utility in the diagnosis of anaphylaxis to benzylisoquinolines

BACKGROUND

Investigation of immediate hypersensitivity reactions in the perioperative setting involves skin testing and measurement of specific IgE (sIgE) as standard practice. In the case of the neuromuscular blocking agents (NMBAs), the main allergenic epitopes have been shown to be substituted ammonium groups. Commercial assays are available for detection of sIgE to these epitopes using morphine and pholcodine substrates but questions have been raised about the effectiveness of these assays in the diagnosis of benzylisoquinoline anaphylaxis. This study was therefore undertaken to assess the effectiveness of these assays in the diagnosis of hypersensitivity reactions to this group of NMBAs.

METHODS

Analysis was carried out on all available results for patients assessed at the Royal North Shore Hospital Anaesthetic Allergy Clinic during the period June 2009 to June 2016. Standardised intradermal skin tests were performed with a panel of NMBAs. Measurement of sIgE to morphine and pholcodine was performed via the Phadia ImmunoCAP^® system.

RESULTS

For all patients with positive skin test results to NMBAs which included a benzylisoquinoline NMBA (n = 24), 75% exhibited negative sIgE to both morphine and pholcodine. Where patients were reactive to benzylisoquinoline NMBAs alone (n = 12), 100% exhibited negative sIgE results, indicating 0% sensitivity of the assays relative to skin testing, in this subgroup.

CONCLUSION

Use of sIgE testing to morphine and pholcodine in the assessment of NMBA immediate hypersensitivity is a valuable tool particularly in the case of reactions to the aminosteroid NMBAs. However, these assays are unreliable in detecting sensitisation to benzylisoquinoline NMBAs.

The effect of farrowing duration and parity on preovulatory follicular size and oxytocin release of sows at subsequent oestrus

This study examined the extent to which prolonged farrowing and parity are associated with plasma oxytocin concentrations and follicular development of oestrous sows during subsequent insemination. A total of 30 sows were allocated to two groups based on farrowing duration: (i) SHORT (n = 14): 159 ± 29 min, (ii) LONG (n = 16): 533 ± 190 min. The sows were also divided into two parity classes: (i) YOUNG (n = 14): parity 2.5 ± 0.8, (ii) OLD (n = 16): parity 6.4 ± 2.3. After weaning, the ovaries were examined daily with transrectal ultrasound. On the second day of oestrus, blood samples were collected for oxytocin (OT) assay at -15, -10, -5, 0, +1, +2, +3, +4, +6, +8, +10, +15, +20, +25, +30, +40, +50 and +60 min with a boar contact between 0 and +10 min. Boar presence stimulated an increase in OT concentrations (p < .05). During boar presence, OT in the LONG group was higher than in the SHORT group (p < .01). The sows in the OLD group had a longer farrowing duration than in the YOUNG group (p < .05). OT levels and diameters of follicles were more relevant for parity than was the duration of farrowing. We therefore conclude that the OT levels and follicular development of oestrous sows are associated due to parity but difficult to be predicted from the duration of previous farrowing.

Abstract P2-06-01: Molecular characterization of human malignant phyllodes tumors reveals potential targeted approaches

Malignant phyllodes tumor (MPT) which belong to the fibroepithelial neoplasm spectrum is a rare type of breast malignancy, and currently there is no effective targeted approach available for MPT. In this study, we tried to identify key genomic alterations and biologic pathways in MPT by whole exome and RNA sequencing of nine MPT tissues. Whole exome sequencing revealed somatic alterations in EGFR, MED12, PIK3CA, PIK3R1, PDGFRA, PDGFRB, PTEN, and TP53. Transcriptome sequencing showed dysregulation of ECM-receptor interaction, focal adhesion, and PI3K-Akt signaling in MPTs when compared to normal breast or invasive breast cancer tissues. Based on the transcriptome profiles, the MPTs were classified into two subtypes; fibrous subtype with upregulation of stromal genes such as collagens and epithelial subtype with upregulation of E-cadherin and Claudins. The molecular classification of fibrous and epithelial subtypes was validated in 28 paraffin-embedded MPT tissues. The fibrous subtype showed higher mitotic index and increased risk for recurrence when compared to the epithelial subtype. We established a patient-derived xenograft model from one fibrous subtype MPT which harbored somatic mutation in PIK3R1 and PDGFRB. In that model, targeted treatment against PIK3CA/mTOR and PDGFR pathways effectively suppressed the tumor growth in vivo. Our data provide insights on the biologic understanding of MPT and suggest a clinically relevant molecular classification. Furthermore, we show that developing effective targeted approaches in MPT can be possible with genomic profiles and patient-derived xenograft models. The clinical efficacy of targeting PDGFR and PIK3CA/mTOR pathways in MPT should be tested in future clinical trials.

Citation Format: Moon H-G, Yun J, Hong BS, Lee E, Lee H-B, Han W, Kim J-I, Noh D-Y, Heo W, Hur S, Kang W, Lee C. Molecular characterization of human malignant phyllodes tumors reveals potential targeted approaches [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-06-01.