Single-Cell Transcriptome Atlas of Murine Endothelial Cells.

The heterogeneity of endothelial cells (ECs) across tissues remains incompletely inventoried. We constructed an atlas of >32,000 single-EC transcriptomes from 11 mouse tissues and identified 78 EC subclusters, including Aqp7+ intestinal capillaries and angiogenic ECs in healthy tissues. ECs from brain/testis, liver/spleen, small intestine/colon, and skeletal muscle/heart pairwise expressed partially overlapping marker genes. Arterial, venous, and lymphatic ECs shared more markers in more tissues than did heterogeneous capillary ECs. ECs from different vascular beds (arteries, capillaries, veins, lymphatics) exhibited transcriptome similarity across tissues, but the tissue (rather than the vessel) type contributed to the EC heterogeneity. Metabolic transcriptome analysis revealed a similar tissue-grouping phenomenon of ECs and heterogeneous metabolic gene signatures in ECs between tissues and between vascular beds within a single tissue in a tissue-type-dependent pattern. The EC atlas taxonomy enabled identification of EC subclusters in public scRNA-seq datasets and provides a powerful discovery tool and resource value.

Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression.

Temporal RNA-sequencing (RNA-seq) studies of bulk samples provide an opportunity for improved understanding of gene regulation during dynamic phenomena such as development, tumor progression or response to an incremental dose of a pharmacotherapeutic. Moreover, single-cell RNA-seq (scRNA-seq) data implicitly exhibit temporal characteristics because gene expression values recapitulate dynamic processes such as cellular transitions. Unfortunately, temporal RNA-seq data continue to be analyzed by methods that ignore this ordinal structure and yield results that are often difficult to interpret. Here, we present Error Modelled Gene Expression Analysis (EMOGEA), a framework for analyzing RNA-seq data that incorporates measurement uncertainty, while introducing a special formulation for those acquired to monitor dynamic phenomena. This method is specifically suited for RNA-seq studies in which low-count transcripts with small-fold changes lead to significant biological effects. Such transcripts include genes involved in signaling and non-coding RNAs that inherently exhibit low levels of expression. Using simulation studies, we show that this framework down-weights samples that exhibit extreme responses such as batch effects allowing them to be modeled with the rest of the samples and maintain the degrees of freedom originally envisioned for a study. Using temporal experimental data, we demonstrate the framework by extracting a cascade of gene expression waves from a well-designed RNA-seq study of zebrafish embryogenesis and an scRNA-seq study of mouse pre-implantation and provide unique biological insights into the regulation of genes in each wave. For non-ordinal measurements, we show that EMOGEA has a much higher rate of true positive calls and a vanishingly small rate of false negative discoveries compared to common approaches. Finally, we provide two packages in Python and R that are self-contained and easy to use, including test data.

ProteomicsDB: toward a FAIR open-source resource for life-science research.

ProteomicsDB (https://www.ProteomicsDB.org) is a multi-omics and multi-organism resource for life science research. In this update, we present our efforts to continuously develop and expand ProteomicsDB. The major focus over the last two years was improving the findability, accessibility, interoperability and reusability (FAIR) of the data as well as its implementation. For this purpose, we release a new application programming interface (API) that provides systematic access to essentially all data in ProteomicsDB. Second, we release a new open-source user interface (UI) and show the advantages the scientific community gains from such software. With the new interface, two new visualizations of protein primary, secondary and tertiary structure as well an updated spectrum viewer were added. Furthermore, we integrated ProteomicsDB with our deep-neural-network Prosit that can predict the fragmentation characteristics and retention time of peptides. The result is an automatic processing pipeline that can be used to reevaluate database search engine results stored in ProteomicsDB. In addition, we extended the data content with experiments investigating different human biology as well as a newly supported organism.

Mental health of Scandinavians during the first lockdown in the COVID-19 pandemic: Psychosocial resources and coping strategies as protective or risk factors for anxiety and depression.

BACKGROUND: The COVID-19 pandemic was a global health and economic crisis. In the early phase of the pandemic, studies found that populations were reporting lower levels of mental well-being and high levels of distress and worry. This study investigated potential protective and risk factors such as sociodemographics and psychological factors such as adaptation/coping. METHODS: Two convenience samples from Norway and Denmark were recruited during the early phase of the first lockdown in May 2020 using snowball sampling primarily by social media. Measures included the Patient Health Questionnaire-4 (PHQ-4) for screening anxiety and depression, COVID-19 distress, and coping strategies applied during the lockdown. Descriptive analyses were applied as well as bivariate correlations for associations between coping and mental health measures. RESULTS: Levels of anxiety and depression were not alarmingly high, but being young, single, and female constituted a higher risk for poorer mental health. Applying positive reframing strategies was negatively associated with poor mental health and high COVID-19 stress, whereas distraction coping strategies were positively correlated with poor mental health and high COVID-19 stress. CONCLUSION: Applying positive reframing as a coping strategy may constitute a protective factor for mental health in the early phase of a crisis such as a pandemic. This knowledge may inform public health agencies on how to promote mental health in similar situations in the future. However, longitudinal and qualitative studies are needed to investigate the long-term effects of the different coping strategies applied.

Small intestine necrosis in catastrophic antiphospholipid syndrome: A rare and severe case.

Catastrophic antiphospholipid syndrome (CAPS) is a multisystem autoimmune disease with widespread thrombotic events. In this case report, we present a young man with primary antiphospholipid syndrome (PAPS) admitted to the hospital with abdominal pain and vomiting. Abdominal computed tomography showed pneumoperitoneum and acute explorative laparotomy revealed small intestinal necrosis indicating small vessel thrombosis without involvement of large intestine. "Triple therapy" was initiated after surgery and the patient was treated in an intensive care unit for 72 days before being discharged to a rehabilitation clinic. A review of the literature regarding CAPS affecting small intestine shows it is extremely rare and may be associated with higher mortality.

BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization.

The amount of biological data, generated with (single cell) omics technologies, is rapidly increasing, thereby exacerbating bottlenecks in the data analysis and interpretation of omics experiments. Data mining platforms that facilitate non-bioinformatician experimental scientists to analyze a wide range of experimental designs and data types can alleviate such bottlenecks, aiding in the exploration of (newly generated or publicly available) omics datasets. Here, we present BIOMEX, a browser-based software, designed to facilitate the Biological Interpretation Of Multi-omics EXperiments by bench scientists. BIOMEX integrates state-of-the-art statistical tools and field-tested algorithms into a flexible but well-defined workflow that accommodates metabolomics, transcriptomics, proteomics, mass cytometry and single cell data from different platforms and organisms. The BIOMEX workflow is accompanied by a manual and video tutorials that provide the necessary background to navigate the interface and get acquainted with the employed methods. BIOMEX guides the user through omics-tailored analyses, such as data pretreatment and normalization, dimensionality reduction, differential and enrichment analysis, pathway mapping, clustering, marker analysis, trajectory inference, meta-analysis and others. BIOMEX is fully interactive, allowing users to easily change parameters and generate customized plots exportable as high-quality publication-ready figures. BIOMEX is open source and freely available at https://www.vibcancer.be/software-tools/biomex.

Evaluation of Myeloperoxidase as Target for Host-Directed Therapy in Tuberculosis In Vivo.

Due to the rise of tuberculosis cases infected with multi and extensively drug-resistant Mycobacterium tuberculosis strains and the emergence of isolates resistant to antibiotics newly in clinical use, host-directed therapies targeting pathogenesis-associated immune pathways adjunct to antibiotics may ameliorate disease and bacterial clearance. Active tuberculosis is characterized by neutrophil-mediated lung pathology and tissue destruction. Previously, we showed that preventing M. tuberculosis induced necrosis in human neutrophils by inhibition of myeloperoxidase (MPO) promoted default apoptosis and subsequent control of mycobacteria by macrophages taking up the mycobacteria-infected neutrophils. To translate our findings in an in vivo model, we tested the MPO inhibitor 4-aminobenzoic acid hydrazide (ABAH) in C3HeB/FeJ mice, which are highly susceptible to M. tuberculosis infection manifesting in neutrophil-associated necrotic granulomas. MPO inhibition alone or as co-treatment with isoniazid, a first-line antibiotic in tuberculosis treatment, did not result in reduced bacterial burden, improved pathology, or altered infiltrating immune cell compositions. MPO inhibition failed to prevent M. tuberculosis induced neutrophil necrosis in C3Heb/FeJ mice in vivo as well as in murine neutrophils in vitro. In contrast to human neutrophils, murine neutrophils do not respond to M. tuberculosis infection in an MPO-dependent manner. Thus, the murine C3HeB/FeJ model does not fully resemble the pathomechanisms in active human tuberculosis. Consequently, murine infection models of tuberculosis are not necessarily adequate to evaluate host-directed therapies targeting neutrophils in vivo.

Identification of a new subset of lymph node stromal cells involved in regulating plasma cell homeostasis.

Antibody-secreting plasma cells (PCs) arise rapidly during adaptive immunity to control infections. The early PCs are retained within the reactive lymphoid organ where their localization and homeostasis rely on extrinsic factors, presumably produced by local niche cells. While myeloid cells have been proposed to form those niches, the contribution by colocalizing stromal cells has remained unclear. Here, we characterized a subset of fibroblastic reticular cells (FRCs) that forms a dense meshwork throughout medullary cords of lymph nodes (LNs) where PCs reside. This medullary FRC type is shown to be anatomically, phenotypically, and functionally distinct from T zone FRCs, both in mice and humans. By using static and dynamic imaging approaches, we provide evidence that medullary FRCs are the main cell type in contact with PCs guiding them in their migration. Medullary FRCs also represent a major local source of the PC survival factors IL-6, BAFF, and CXCL12, besides also producing APRIL. In vitro, medullary FRCs alone or in combination with macrophages promote PC survival while other LN cell types do not have this property. Thus, we propose that this FRC subset, together with medullary macrophages, forms PC survival niches within the LN medulla, and thereby helps in promoting the rapid development of humoral immunity, which is critical in limiting early pathogen spread.

Single-Cell RNA Sequencing Reveals Renal Endothelium Heterogeneity and Metabolic Adaptation to Water Deprivation.

BACKGROUND: Renal endothelial cells from glomerular, cortical, and medullary kidney compartments are exposed to different microenvironmental conditions and support specific kidney processes. However, the heterogeneous phenotypes of these cells remain incompletely inventoried. Osmotic homeostasis is vitally important for regulating cell volume and function, and in mammals, osmotic equilibrium is regulated through the countercurrent system in the renal medulla, where water exchange through endothelium occurs against an osmotic pressure gradient. Dehydration exposes medullary renal endothelial cells to extreme hyperosmolarity, and how these cells adapt to and survive in this hypertonic milieu is unknown. METHODS: We inventoried renal endothelial cell heterogeneity by single-cell RNA sequencing >40,000 mouse renal endothelial cells, and studied transcriptome changes during osmotic adaptation upon water deprivation. We validated our findings by immunostaining and functionally by targeting oxidative phosphorylation in a hyperosmolarity model in vitro and in dehydrated mice in vivo. RESULTS: We identified 24 renal endothelial cell phenotypes (of which eight were novel), highlighting extensive heterogeneity of these cells between and within the cortex, glomeruli, and medulla. In response to dehydration and hypertonicity, medullary renal endothelial cells upregulated the expression of genes involved in the hypoxia response, glycolysis, and-surprisingly-oxidative phosphorylation. Endothelial cells increased oxygen consumption when exposed to hyperosmolarity, whereas blocking oxidative phosphorylation compromised endothelial cell viability during hyperosmotic stress and impaired urine concentration during dehydration. CONCLUSIONS: This study provides a high-resolution atlas of the renal endothelium and highlights extensive renal endothelial cell phenotypic heterogeneity, as well as a previously unrecognized role of oxidative phosphorylation in the metabolic adaptation of medullary renal endothelial cells to water deprivation.

High spatiotemporal resolution dynamic contrast-enhanced MRI improves the image-based discrimination of histopathology risk groups of peripheral zone prostate cancer: a supervised machine learning approach.

OBJECTIVE: To assess if adding perfusion information from dynamic contrast-enhanced (DCE MRI) acquisition schemes with high spatiotemporal resolution to T2w/DWI sequences as input features for a gradient boosting machine (GBM) machine learning (ML) classifier could better classify prostate cancer (PCa) risk groups than T2w/DWI sequences alone. MATERIALS AND METHODS: One hundred ninety patients (68 ± 9 years) were retrospectively evaluated at 3T MRI for clinical suspicion of PCa. Included were 201 peripheral zone (PZ) PCa lesions. Histopathological confirmation on fusion biopsy was matched with normal prostate parenchyma contralaterally. Biopsy results were grouped into benign tissue and low-, intermediate-, and high-risk groups (Gleason sum score 6, 7, and > 7, respectively). DCE MRI was performed using golden-angle radial sparse MRI. Perfusion maps (Ktrans, Kep, Ve), apparent diffusion coefficient (ADC), and absolute T2w signal intensity were determined and used as input features for building two ML models: GBM with/without perfusion maps. Areas under the receiver operating characteristic curve (AUC) values for correlated models were compared. RESULTS: For the classification of benign vs. malignant and intermediate- vs. high-grade PCa, perfusion information added relevant information (AUC values 1 vs. 0.953 and 0.909 vs. 0.700, p < 0.001 and p = 0.038), while no statistically significant effect was found for low- vs. intermediate- and high-grade PCa. CONCLUSION: Perfusion information from DCE MRI acquisition schemes with high spatiotemporal resolution to ML classifiers enables a superior risk stratification between benign and malignant and intermediate- and high-risk PCa in the PZ compared with classifiers based on T2w/DWI information alone. KEY POINTS: • In the recent guidelines, the role of DCE MRI has changed from a mandatory to recommended sequence. • DCE MRI acquisition schemes with high spatiotemporal resolution (e.g., GRASP) have been shown to improve the diagnostic performance compared with conventional DCE MRI sequences. • Using perfusion information acquired with GRASP in combination with ML classifiers significantly improved the prediction of benign vs. malignant and intermediate- vs. high-grade peripheral zone prostate cancer compared with non-contrast sequences.

Minority migrant men's attitudes toward female genital mutilation: Developing strategies to engage men.

This article explores minority migrant men's attitudes towards female genital mutilation (FGM), and how these attitudes can be used to develop strategies to engage men in the eradication of FGM. Based on interviews and focus group discussions, the article finds that men's attitudes can be enabling, disabling or neutral: the identification of and variations between these need to be taken into account when developing strategies to engage men in the eradication of FGM. There is currently a window of opportunity for involving minority migrant men in the prevention of FGM and in the challenging of a minority migrant gender regime.

Gadoxetate Disodium versus Gadoterate Meglumine: Quantitative Respiratory and Hemodynamic Metrics by Using Compressed-Sensing MRI.

Background Gadoxetate disodium has been associated with various respiratory irregularities at arterial imaging MRI. Purpose To measure the relationship between gadolinium-based contrast agent administration and irregularities by comparing gadoxetate disodium and gadoterate meglumine at free breathing. Materials and Methods This prospective observational cohort study (January 2015 to May 2017) included consecutive abdominal MRI performed with either gadoxetate disodium or gadoterate meglumine enhancement. Participants underwent dynamic imaging by using the golden-angle radial sparse parallel sequence at free breathing. The quantitative assessment evaluated the aortic contrast enhancement, the respiratory hepatic translation, and the k-space-derived respiratory pattern. Analyses of variance compared hemodynamic metrics, respiratory-induced hepatic motion, and respiratory parameters before and after respiratory gating. Results A total of 497 abdominal MRI examinations were included. Of these, 338 participants were administered gadoxetate disodium (mean age, 59 years ± 15; 153 women) and 159 participants were administered gadoterate meglumine (mean age, 59 years ± 17; 85 women). The arterial bolus of gadoxetate disodium arrived later than gadoterate meglumine (19.7 vs 16.3 seconds, respectively; P < .001). Evaluation of the hepatic respiratory translation showed respiratory motion occurring in 70.7% (239 of 338) of participants who underwent gadoxetate-enhanced examinations and in 28.9% (46 of 159) of participants who underwent gadoterate-enhanced examinations (P < .001). The duration of motion irregularities was longer for gadoxetate than for gadoterate (19.2 seconds vs 17.2 seconds, respectively) and the motion irregularities were more severe (P < .001). Both the respiratory frequency and amplitude were shorter for participants administered gadoxetate from the prebolus phase to the late arterial phase compared with gadoterate (P < .001). Conclusion The administration of two different gadolinium-based contrast agents, gadoxetate and gadoterate, at free-breathing conditions potentially leads to respiratory irregularities with differing intensity and onset. © RSNA, 2019 Online supplemental material is available for this article.

Compressed Sensing Radial Sampling MRI of Prostate Perfusion: Utility for Detection of Prostate Cancer.

Purpose To investigate the diagnostic performance of a dual-parameter approach by combining either volumetric interpolated breath-hold examination (VIBE)- or golden-angle radial sparse parallel (GRASP)-derived dynamic contrast agent-enhanced (DCE) MRI with established diffusion-weighted imaging (DWI) compared with traditional single-parameter evaluations on the basis of DWI alone. Materials and Methods Ninety-four male participants (66 years ± 7 [standard deviation]) were prospectively evaluated at 3.0-T MRI for clinical suspicion of prostate cancer. Included were 101 peripheral zone prostate cancer lesions. Histopathologic confirmation at MRI transrectal US fusion biopsy was matched with normal contralateral prostate parenchyma. MRI was performed with diffusion weighting and DCE by using GRASP (temporal resolution, 2.5 seconds) or VIBE (temporal resolution, 10 seconds). Perfusion (influx forward volume transfer constant [Ktrans] and rate constant [Kep]) and apparent diffusion coefficient (ADC) parameters were determined by tumor volume analysis. Areas under the receiver operating characteristic curve were compared for both sequences. Results Evaluated were 101 prostate cancer lesions (GRASP, 61 lesions; VIBE, 40 lesions). In a combined analysis, diffusion and perfusion parameters ADC with Ktrans or Kep acquired with GRASP had higher diagnostic performance compared with diffusion characteristics alone (area under the curve, 0.97 ± 0.02 [standard error] vs 0.93 ± 0.03; P < .006 and .021, respectively), whereas ADC with perfusion parameters acquired with VIBE had no additional benefit (area under the curve, 0.94 ± 0.03 vs 0.93 ± 0.04; P = .18and .50, respectively, for combination of ADC with Ktrans and Kep). Conclusion If used in a dual-parameter model, incorporating diffusion and perfusion characteristics, the golden-angle radial sparse parallel acquisition technique improves the diagnostic performance of multiparametric MRI examinations of the prostate. This effect could not be observed combining diffusing with perfusion parameters acquired with volumetric interpolated breath-hold examination. © RSNA, 2018.

A Manual Bristleless Toothbrush Demonstrates Slight Improvement in Gingival Recession Compared to a Conventional Soft Manual Brush.

PURPOSE: This randomized clinical trial tested whether a novel bristleless toothbrush design is more effective in preventing gingival recession in adults receiving periodontal maintenance than is a soft toothbrush with nylon bristles. MATERIALS AND METHODS: Twenty-three subjects with gingival recession were recruited who received regular periodontal maintenance care at Western University of Health Sciences Dental Center, and who did not exhibit signs of acute dental or systemic disease, occlusal discrepancies or parafunctional habits. These subjects were randomly assigned to to two groups, one using a soft nylon-bristled toothbrush, and the other using the experimental toothbrush that contains a brush head with short, soft, rubbery cones. Both groups received regular periodontal maintenance and periodontal exams by blinded examiners every 3-4 months, measuring probing depth, bleeding on probing, and plaque indices. Gingival recession was assessed clinically and through use of a stent on diagnostic casts obtained at each visit. RESULTS: Average probing depths, plaque levels, and the number of sites with bleeding on probing did not change over at least 9 months. After 9 months, there was a small but statistically significant improvement in gingival recession (0.4 mm, p < 0.01) at sites with gingival recession in the experimental toothbrush group compared to the control group. CONCLUSION: In periodontal maintenance patients, the bristleless toothbrush used in this study was as effective in plaque removal and prevention of gingival inflammation than a conventional toothbrush with soft nylon bristles, while increasing the possibility of gingival tissue rebound over denuded root surfaces.

Comparison of conventional DCE-MRI and a novel golden-angle radial multicoil compressed sensing method for the evaluation of breast lesion conspicuity.

PURPOSE: To compare a novel multicoil compressed sensing technique with flexible temporal resolution, golden-angle radial sparse parallel (GRASP), to conventional fat-suppressed spoiled three-dimensional (3D) gradient-echo (volumetric interpolated breath-hold examination, VIBE) MRI in evaluating the conspicuity of benign and malignant breast lesions. MATERIALS AND METHODS: Between March and August 2015, 121 women (24-84 years; mean, 49.7 years) with 180 biopsy-proven benign and malignant lesions were imaged consecutively at 3.0 Tesla in a dynamic contrast-enhanced (DCE) MRI exam using sagittal T1-weighted fat-suppressed 3D VIBE in this Health Insurance Portability and Accountability Act-compliant, retrospective study. Subjects underwent MRI-guided breast biopsy (mean, 13 days [1-95 days]) using GRASP DCE-MRI, a fat-suppressed radial "stack-of-stars" 3D FLASH sequence with golden-angle ordering. Three readers independently evaluated breast lesions on both sequences. Statistical analysis included mixed models with generalized estimating equations, kappa-weighted coefficients and Fisher's exact test. RESULTS: All lesions demonstrated good conspicuity on VIBE and GRASP sequences (4.28 ± 0.81 versus 3.65 ± 1.22), with no significant difference in lesion detection (P = 0.248). VIBE had slightly higher lesion conspicuity than GRASP for all lesions, with VIBE 12.6% (0.63/5.0) more conspicuous (P < 0.001). Masses and nonmass enhancement (NME) were more conspicuous on VIBE (P < 0.001), with a larger difference for NME (14.2% versus 9.4% more conspicuous). Malignant lesions were more conspicuous than benign lesions (P < 0.001) on both sequences. CONCLUSION: GRASP DCE-MRI, a multicoil compressed sensing technique with high spatial resolution and flexible temporal resolution, has near-comparable performance to conventional VIBE imaging for breast lesion evaluation. LEVEL OF EVIDENCE: 3 Technical Efficacy: Stage 3 J. MAGN. RESON. IMAGING 2017;45:1746-1752.

Exploring the potential of high resolution mass spectrometry for the investigation of lignin-derived phenol substitutes in phenolic resin syntheses.

Chemical degradation is an efficient method to obtain bio-oils and other compounds from lignin. Lignin bio-oils are potential substitutes for the phenol component of phenol formaldehyde (PF) resins. Here, we developed an analytical method based on high resolution mass spectrometry that provided structural information for the synthesized lignin-derived resins and supported the prediction of their properties. Different model resins based on typical lignin degradation products were analyzed by electrospray ionization in negative ionization mode. Utilizing enhanced mass defect filter techniques provided detailed structural information of the lignin-based model resins and readily complemented the analytical data from differential scanning calorimetry and thermogravimetric analysis. Relative reactivity and chemical diversity of the phenol substitutes were significant determinants of the outcome of the PF resin synthesis and thus controlled the areas of application of the resulting polymers. Graphical abstract ᅟ.

Trapping of naive lymphocytes triggers rapid growth and remodeling of the fibroblast network in reactive murine lymph nodes.

Adaptive immunity is initiated in T-cell zones of secondary lymphoid organs. These zones are organized in a rigid 3D network of fibroblastic reticular cells (FRCs) that are a rich cytokine source. In response to lymph-borne antigens, draining lymph nodes (LNs) expand several folds in size, but the fate and role of the FRC network during immune response is not fully understood. Here we show that T-cell responses are accompanied by the rapid activation and growth of FRCs, leading to an expanded but similarly organized network of T-zone FRCs that maintains its vital function for lymphocyte trafficking and survival. In addition, new FRC-rich environments were observed in the expanded medullary cords. FRCs are activated within hours after the onset of inflammation in the periphery. Surprisingly, FRC expansion depends mainly on trapping of naïve lymphocytes that is induced by both migratory and resident dendritic cells. Inflammatory signals are not required as homeostatic T-cell proliferation was sufficient to trigger FRC expansion. Activated lymphocytes are also dispensable for this process, but can enhance the later growth phase. Thus, this study documents the surprising plasticity as well as the complex regulation of FRC networks allowing the rapid LN hyperplasia that is critical for mounting efficient adaptive immunity.

Crown Lengthening Needs and Outcomes in Adults Attending a Predoctoral Clinic.

In this retrospective study of 5,536 patients admitted over four years at a predoctoral dental clinic for comprehensive care, general dentists identified crown lengthening needs in 584 patients and 760 teeth. Only 51 patients and 68 teeth actually received crown lengthening procedures. For the other cases, patients discontinued treatment or chose extraction or restoration without crown lengthening procedures. Teeth that received crown lengthening procedures were most likely restored and functioning for at least one year.

Enhanced Mass Defect Filtering To Simplify and Classify Complex Mixtures of Lignin Degradation Products.

High resolution mass spectrometry was utilized to study the highly complex product mixtures resulting from electrochemical breakdown of lignin. As most of the chemical structures of the degradation products were unknown, enhanced mass defect filtering techniques were implemented to simplify the characterization of the mixtures. It was shown that the implemented ionization techniques had a major impact on the range of detectable breakdown products, with atmospheric pressure photoionization in negative ionization mode providing the widest coverage in our experiments. Different modified Kendrick mass plots were used as a basis for mass defect filtering, where Kendrick mass defect and the mass defect of the lignin-specific guaiacol (C7H7O2) monomeric unit were utilized, readily allowing class assignments independent of the oligomeric state of the product. The enhanced mass defect filtering strategy therefore provided rapid characterization of the sample composition. In addition, the structural similarities between the compounds within a degradation sequence were determined by comparison to a tentatively identified product of this compound series. In general, our analyses revealed that primarily breakdown products with low oxygen content were formed under electrochemical conditions using protic ionic liquids as solvent for lignin.

Global transcription of CRISPR loci in the human oral cavity.

BACKGROUND: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are active in acquired resistance against bacteriophage and plasmids in a number of environments. In the human mouth, CRISPR loci evolve to counteract oral phage, but the expression of these CRISPR loci has not previously been investigated. We sequenced cDNA from CRISPR loci found in numerous different oral bacteria and compared with oral phage communities to determine whether the transcription of CRISPR loci is specifically targeted towards highly abundant phage present in the oral environment. RESULTS: We found that of the 529,027 CRISPR spacer groups studied, 88 % could be identified in transcripts, indicating that the vast majority of CRISPR loci in the oral cavity were transcribed. There were no strong associations between CRISPR spacer repertoires and oral health status or nucleic acid type. We also compared CRISPR repertoires with oral bacteriophage communities, and found that there was no significant association between CRISPR transcripts and oral phage, regardless of the CRISPR type being evaluated. We characterized highly expressed CRISPR spacers and found that they were no more likely than other spacers to match oral phage. By reassembling the CRISPR-bearing reads into longer CRISPR loci, we found that the majority of the loci did not have spacers matching viruses found in the oral cavities of the subjects studied. For some CRISPR types, loci containing spacers matching oral phage were significantly more likely to have multiple spacers rather than a single spacer matching oral phage. CONCLUSIONS: These data suggest that the transcription of oral CRISPR loci is relatively ubiquitous and that highly expressed CRISPR spacers do not necessarily target the most abundant oral phage.