Programs for the persistence, vigilance and control of human CD8+ lung-resident memory T cells.

Tissue-resident memory T cells (TRM cells) in the airways mediate protection against respiratory infection. We characterized TRM cells expressing integrin αE (CD103) that reside within the epithelial barrier of human lungs. These cells had specialized profiles of chemokine receptors and adhesion molecules, consistent with their unique localization. Lung TRM cells were poised for rapid responsiveness by constitutive expression of deployment-ready mRNA encoding effector molecules, but they also expressed many inhibitory regulators, suggestive of programmed restraint. A distinct set of transcription factors was active in CD103+ TRM cells, including Notch. Genetic and pharmacological experiments with mice revealed that Notch activity was required for the maintenance of CD103+ TRM cells. We have thus identified specialized programs underlying the residence, persistence, vigilance and tight control of human lung TRM cells.

Evaluating cone cut in rectangular collimation in intraoral radiography: application of ALADA and radiation stewardship.

OBJECTIVE: Rectangular collimation is a popular method used in intraoral radiography to reduce patient exposure to ionizing radiation. One of the perceived drawbacks of rectangular collimation is the possibility of an increase in cone cut errors ultimately impacting the diagnostic value of the radiographs. Thus, the aim of this study was to explore the frequency of cone cut errors in radiographs taken using a rectangular collimator. MATERIALS AND METHODS: Radiographs taken using PSP plates at Academic Center for Dentistry Amsterdam in the Netherlands by staff and students from January to December 2015 were assessed for cone cut errors. The radiographs were grouped as bitewings, front teeth, inferior premolars and molars, and superior premolars and molars and categorized as no cone cut, cone cut but diagnostically usable, and cone cut but diagnostically not usable. The results were entered into Microsoft Excel and analyzed thereafter. RESULTS: A total of 53,684 radiographs were assessed, 79% had no cone cut errors and consequently 21% had some degree of cone cut. However, the diagnostic value was unaffected in 18% of the radiographs with cone cut. Only 3% of the radiographs were deemed diagnostically unusable due to cone cut. The most common area of cone cut was in the premolar and molar areas while cone cut in the front teeth was least likely to be diagnostically unusable. CONCLUSION: Cone cut from the use of a rectangular collimator does not seem to result in an increase of diagnostically unusable radiographs. Thus, rectangular collimation should be preferred as it decreases the amount of radiation exposure to the patient while producing diagnostically usable radiographs and thus allowing the dental professional to adhere to the ALADA principle and practice radiation stewardship. CLINICAL RELEVANCE: Scientific rationale for the study: rectangular collimation is a method used to reduce patient exposure to ionizing radiation; however, this benefit is negligible if radiographs must be retaken due to cone cut errors that make the radiograph diagnostically unusable. Therefore, the aim of this study was to explore the frequency of cone cut in radiographs taken using a rectangular collimator. PRINCIPAL FINDINGS: cone cut was observed in 21% of the radiographs; however, only 3% of the radiographs were considered diagnostically unusable. PRACTICAL IMPLICATIONS: rectangular collimation does not result in a high number of diagnostically unusable radiographs and should be used to reduce patient exposure to ionizing radiation.

External Validation and Comparison of Clostridioides difficile Severity Scoring Systems.

BACKGROUND: Many models have been developed to predict severe outcomes from Clostridioides difficile infection (CDI). These models are usually developed at a single institution and largely are not externally validated. Our aim in this study was to validate previously published risk scores in a multicenter cohort of patients with CDI. METHODS: This was a retrospective study on 4 inpatient cohorts with CDI from 3 distinct sites: the universities of Michigan (2010-2012 and 2016), Chicago (2012), and Wisconsin (2012). The primary composite outcome was admission to an intensive care unit, colectomy, and/or death attributed to CDI within 30 days of positive testing. Both within each cohort and combined across all cohorts, published CDI severity scores were assessed and compared to each other and the Infectious Diseases Society of America (IDSA) guideline definitions of severe and fulminant CDI. RESULTS: A total of 3646 patients were included for analysis. Including the 2 IDSA guideline definitions, 14 scores were assessed. Performance of scores varied within each cohort and in the combined set (mean area under the receiver operator characteristic curve [AuROC], 0.61; range, 0.53-0.66). Only half of the scores had performance at or better than IDSA severe and fulminant definitions (AuROCs of 0.64 and 0.63, respectively). Most of the scoring systems had more false than true positives in the combined set (mean, 81.5%; range, 0%-91.5%). CONCLUSIONS: No published CDI severity score showed stable, good predictive ability for adverse outcomes across multiple cohorts/institutions or in a combined multicenter cohort.

Core circadian clock genes Per1 and Per2 regulate the rhythm in photoreceptor outer segment phagocytosis.

Retinal photoreceptors undergo daily renewal of their distal outer segments, a process indispensable for maintaining retinal health. Photoreceptor outer segment (POS) phagocytosis occurs as a daily peak, roughly about 1 hour after light onset. However, the underlying cellular and molecular mechanisms which initiate this process are still unknown. Here we show that, under constant darkness, mice deficient for core circadian clock genes (Per1 and Per2) lack a daily peak in POS phagocytosis. By qPCR analysis, we found that core clock genes were rhythmic over 24 hours in both WT and Per1, Per2 double mutant whole retinas. More precise transcriptomics analysis of laser capture microdissected WT photoreceptors revealed no differentially expressed genes between time points preceding and during the peak of POS phagocytosis. In contrast, we found that microdissected WT retinal pigment epithelium (RPE) had a number of genes that were differentially expressed at the peak phagocytic time point compared to adjacent ones. We also found a number of differentially expressed genes in Per1, Per2 double mutant RPE compared to WT ones at the peak phagocytic time point. Finally, based on STRING analysis, we found a group of interacting genes that potentially drive POS phagocytosis in the RPE. This potential pathway consists of genes such as: Pacsin1, Syp, Camk2b, and Camk2d among others. Our findings indicate that Per1 and Per2 are necessary clock components for driving POS phagocytosis and suggest that this process is transcriptionally driven by the RPE.

Protecting my injured child: a qualitative study of parents' experience of caring for a child with a displaced distal radius fracture.

BACKGROUND: Childhood fractures can have a significant impact on the daily lives of families affecting children's normal activities and parent's work. Wrist fractures are the most common childhood fracture. The more serious wrist fractures, that can look visibly bent, are often treated with surgery to realign the bones; but this may not be necessary as bent bones straighten in growing children. The children's radius acute fracture fixation trial (CRAFFT) is a multicentre randomised trial of surgery versus a cast without surgery for displaced wrist fractures. Little is known about how families experience these wrist fractures and how they manage treatment uncertainty. This study aimed to understand families' experience of this injury and what it is like to be asked to include their child in a clinical trial. METHODS: Nineteen families (13 mothers, 7 fathers, 2 children) from across the UK participated in telephone interviews. Interviews were audio recorded, transcribed and analysed using reflexive thematic analysis. RESULTS: Our findings highlight parents' desire to be a good parent through the overarching theme "protecting my injured child". To protect their child after injury, parents endeavoured to make the right decisions about treatment and provide comfort to their child but they experienced ongoing worry about their child's recovery. Our findings show that parents felt responsible for the decision about their child's treatment and their child's recovery. They also reveal the extent to which parents worried about the look of their child's wrist and their need for reassurance that the wrist was healing. CONCLUSION: Our findings show that protecting their child after injury can be challenging for parents who need support to make decisions about treatment and confidently facilitate their child's recovery. They also highlight the importance of providing information about treatments, acknowledging parents' concerns and their desire to do the right thing for their child, reassuring parents that their child's wrist will heal and ensuring parents understand what to expect as their child recovers.

ACCURACY OF CLINICAL AND RADIOGRAPHIC MEASUREMENTS OF PERIODONTAL INFRABONY DEFECTS OF DIAGNOSTIC TEST ACCURACY (DTA) STUDIES: A SYSTEMATIC REVIEW AND META-ANALYSIS.

BACKGROUND: The aim of this study was to determine the accuracy of clinical and radiographic measurements of infrabony periodontal defects. METHODS: The MEDLINE-Pubmed and Cochrane-CENTRAL electronic databases were searched from initiation to May 2020. The inclusion criteria were clinical trials, human subjects with at least one infrabony defect, measurements of clinical attachment level (CAL), radiographic bone level (rBL), and intraoperative bone level (iBL) used as the reference standard. RESULTS: In total, 11 studies including 17 comparisons were included in this meta-analysis. All 17 comparisons showed that the values of the CAL and rBL measurements underestimated the iBL values. For CAL, the analysis showed a significant difference of means of -1.22 (P < .00001; 95%CI: [-1.49; -0.95]) and for rBL -1.10 (P < .00001; 95%CI: [-1.34; -0.85]). No significant DiffM were observed between the CAL and rBL measurements (DiffM -0.05; P = .76; 95%CI: [-0.39; 0.28]). CONCLUSION: The results of this systematic review and meta-analysis show that both clinical and radiographic measurements substantially underestimate the bone level when compared to intraoperative level measurements. However, there was no significant difference in the results between the clinical attachment level measurements and the radiographic observation.

Changes in the Association Between Diagnostic Testing Method, Polymerase Chain Reaction Ribotype, and Clinical Outcomes From Clostridioides difficile Infection: One Institution's Experience.

BACKGROUND: In Clostridioides difficile infection (CDI), the relationship between clinical, microbial, and temporal/epidemiological trends, disease severity and adverse outcomes is incompletely understood. In a follow-up to our study from 2010-2013, we evaluate stool toxin levels and C. difficile polymerase chain reaction (PCR) ribotypes. We hypothesized that elevated stool toxins and infection with ribotype 027 associate with adverse outcomes. METHODS: In 565 subjects at the University of Michigan with CDI diagnosed by positive testing for toxins A/B by enzyme immunoassay (EIA) or PCR for the tcdB gene, we quantified stool toxin levels via a modified cell cytotoxicity assay (CCA), isolated C. difficile by anaerobic culture, and performed PCR ribotyping. Severe CDI was defined by Infectious Diseases Society of America (IDSA) criteria, and primary outcomes were all-cause 30-day mortality and a composite of colectomy, intensive care unit admission, and/or death attributable to CDI within 30 days. Analyses included bivariable tests and logistic regression. RESULTS: 199 samples were diagnosed by EIA; 447 were diagnosed by PCR. Toxin positivity associated with IDSA severity but not primary outcomes. In 2016, compared with 2010-2013, ribotype 106 newly emerged, accounting for 10.6% of strains, ribotype 027 fell from 16.5% to 9.3%, and ribotype 014-027 remained stable at 18.9%. Ribotype 014-020 associated with IDSA severity and 30-day mortality (P = .001). CONCLUSIONS: Toxin positivity by EIA and CCA associated with IDSA severity but not with subsequent adverse outcomes. The molecular epidemiology of C. difficile has shifted, which may have implications for the optimal diagnostic strategy for and clinical severity of CDI.

Improving CLL Vγ9Vδ2-T-cell fitness for cellular therapy by ex vivo activation and ibrutinib.

The efficacy of autologous (αß) T-cell-based treatment strategies in chronic lymphocytic leukemia (CLL) has been modest. The Vγ9Vδ2-T cell subset consists of cytotoxic T lymphocytes with potent antilymphoma activity via a major histocompatibility complex-independent mechanism. We studied whether Vγ9Vδ2-T cells can be exploited as autologous effector lymphocytes in CLL. Healthy control Vγ9Vδ2-T cells were activated by and had potent cytolytic activity against CLL cells. However, CLL-derived Vγ9Vδ2-T cells proved dysfunctional with respect to effector cytokine production and degranulation, despite an increased frequency of the effector-type subset. Consequently, cytotoxicity against malignant B cells was hampered. A comparable dysfunctional phenotype was observed in healthy Vγ9Vδ2-T cells after coculture with CLL cells, indicating a leukemia-induced mechanism. Gene-expression profiling implicated alterations in synapse formation as a conceivable contributor to compromised Vγ9Vδ2-T-cell function in CLL patients. Dysfunction of Vγ9Vδ2-T cells was fully reversible upon activation with autologous monocyte-derived dendritic cells (moDCs). moDC activation resulted in efficient expansion and predominantly yielded Vγ9Vδ2-T cells with a memory phenotype. Furthermore, ibrutinib treatment promoted an antitumor T helper 1 (TH1) phenotype in Vγ9Vδ2-T cells, and we demonstrated binding of ibrutinib to IL-2-inducible kinase (ITK) in Vγ9Vδ2-T cells. Taken together, CLL-mediated dysfunction of autologous Vγ9Vδ2-T cells is fully reversible, resulting in potent cytotoxicity toward CLL cells. Our data support the potential use of Vγ9Vδ2-T cells as effector T cells in CLL immunotherapy and favor further exploration of combining Vγ9Vδ2-T-cell-based therapy with ibrutinib.

Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer.

BACKGROUND: Estrogen receptor (ER) positive breast cancer is often effectively treated with drugs that inhibit ER signaling, i.e., tamoxifen (TAM) and aromatase inhibitors (AIs). However, 30% of ER+ breast cancer patients develop resistance to therapy leading to tumour recurrence. Changes in the methylation profile have been implicated as one of the mechanisms through which therapy resistance develops. Therefore, we aimed to identify methylation loci associated with endocrine therapy resistance. METHODS: We used genome-wide DNA methylation profiles of primary ER+/HER2- tumours from The Cancer Genome Atlas in combination with curated data on survival and treatment to predict development of endocrine resistance. Association of individual DNA methylation markers with survival was assessed using Cox proportional hazards models in a cohort of ER+/HER2- tumours (N = 552) and two sub-cohorts corresponding to the endocrine treatment (AI or TAM) that patients received (N = 210 and N = 172, respectively). We also identified multivariable methylation signatures associated with survival using Cox proportional hazards models with elastic net regularization. Individual markers and multivariable signatures were compared with DNA methylation profiles generated in a time course experiment using the T47D ER+ breast cancer cell line treated with tamoxifen or deprived from estrogen. RESULTS: We identified 134, 5 and 1 CpGs for which DNA methylation is significantly associated with survival in the ER+/HER2-, TAM and AI cohorts respectively. Multi-locus signatures consisted of 203, 36 and 178 CpGs and showed a large overlap with the corresponding single-locus signatures. The methylation signatures were associated with survival independently of tumour stage, age, AI treatment, and luminal status. The single-locus signature for the TAM cohort was conserved among the loci that were differentially methylated in endocrine-resistant T47D cells. Similarly, multi-locus signatures for the ER+/HER2- and AI cohorts were conserved in endocrine-resistant T47D cells. Also at the gene set level, several sets related to endocrine therapy and resistance were enriched in both survival and T47D signatures. CONCLUSIONS: We identified individual and multivariable DNA methylation markers associated with therapy resistance independently of luminal status. Our results suggest that these markers identified from primary tumours prior to endocrine treatment are associated with development of endocrine resistance.

Histological validation of a type 1 diabetes clinical diagnostic model for classification of diabetes.

AIMS: Misclassification of diabetes is common due to an overlap in the clinical features of type 1 and type 2 diabetes. Combined diagnostic models incorporating clinical and biomarker information have recently been developed that can aid classification, but they have not been validated using pancreatic pathology. We evaluated a clinical diagnostic model against histologically defined type 1 diabetes. METHODS: We classified cases from the Network for Pancreatic Organ donors with Diabetes (nPOD) biobank as type 1 (n = 111) or non-type 1 (n = 42) diabetes using histopathology. Type 1 diabetes was defined by lobular loss of insulin-containing islets along with multiple insulin-deficient islets. We assessed the discriminative performance of previously described type 1 diabetes diagnostic models, based on clinical features (age at diagnosis, BMI) and biomarker data [autoantibodies, type 1 diabetes genetic risk score (T1D-GRS)], and singular features for identifying type 1 diabetes by the area under the curve of the receiver operator characteristic (AUC-ROC). RESULTS: Diagnostic models validated well against histologically defined type 1 diabetes. The model combining clinical features, islet autoantibodies and T1D-GRS was strongly discriminative of type 1 diabetes, and performed better than clinical features alone (AUC-ROC 0.97 vs. 0.95; P = 0.03). Histological classification of type 1 diabetes was concordant with serum C-peptide [median < 17 pmol/l (limit of detection) vs. 1037 pmol/l in non-type 1 diabetes; P < 0.0001]. CONCLUSIONS: Our study provides robust histological evidence that a clinical diagnostic model, combining clinical features and biomarkers, could improve diabetes classification. Our study also provides reassurance that a C-peptide-based definition of type 1 diabetes is an appropriate surrogate outcome that can be used in large clinical studies where histological definition is impossible. Parts of this study were presented in abstract form at the Network for Pancreatic Organ Donors Conference, Florida, USA, 19-22 February 2019 and Diabetes UK Professional Conference, Liverpool, UK, 6-8 March 2019.

Physician perceptions of a multidisciplinary endocarditis team.

Infectious endocarditis is a highly morbid infection that requires coordination of care across medical and surgical specialties, often through the use of a multidisciplinary team model. Multiple studies have demonstrated that such conferences can improve clinical outcomes. However, little is known about physicians' impressions of these groups. We surveyed 126 (response rate of 30%) internal medicine, infectious diseases, cardiology, and cardiac surgery providers 1 year after the implementation of an endocarditis team at the University of Michigan. Ninety-eight percent of physicians felt that the endocarditis team improved communication between specialties. Additionally, over 85% of respondents agreed that the group influenced diagnostic evaluation, reduced management errors, increased access to surgery, and decreased in-hospital mortality for endocarditis patients. These results suggest that multidisciplinary endocarditis teams are valued by physicians as a tool to improve patient care and serve an important role in increasing communication between providers.

Diurnal rhythms in the white adipose tissue transcriptome are disturbed in obese individuals with type 2 diabetes compared with lean control individuals.

AIMS/HYPOTHESIS: Animal studies have indicated that disturbed diurnal rhythms of clock gene expression in adipose tissue can induce obesity and type 2 diabetes. The importance of the circadian timing system for energy metabolism is well established, but little is known about the diurnal regulation of (clock) gene expression in obese individuals with type 2 diabetes. In this study we aimed to identify key disturbances in the diurnal rhythms of the white adipose tissue transcriptome in obese individuals with type 2 diabetes. METHODS: In a case-control design, we included six obese individuals with type 2 diabetes and six healthy, lean control individuals. All participants were provided with three identical meals per day for 3 days at zeitgeber time (ZT, with ZT 0:00 representing the time of lights on) 0:30, 6:00 and 11:30. Four sequential subcutaneous abdominal adipose tissue samples were obtained, on day 2 at ZT 15:30, and on day 3 at ZT 0:15, ZT 5:45 and ZT 11:15. Gene expression was measured using RNA sequencing. RESULTS: The core clock genes showed reduced amplitude oscillations in the individuals with type 2 diabetes compared with the healthy control individuals. Moreover, in individuals with type 2 diabetes, only 1.8% (303 genes) of 16,818 expressed genes showed significant diurnal rhythmicity, compared with 8.4% (1421 genes) in healthy control individuals. Enrichment analysis revealed a loss of rhythm in individuals with type 2 diabetes of canonical metabolic pathways involved in the regulation of lipolysis. Enrichment analysis of genes with an altered mesor in individuals with type 2 diabetes showed decreased activity of the translation initiating pathway 'EIF2 signaling'. Individuals with type 2 diabetes showed a reduced diurnal rhythm in postprandial glucose concentrations. CONCLUSIONS/INTERPRETATION: Diurnal clock and metabolic gene expression rhythms are decreased in subcutaneous adipose tissue of obese individuals with type 2 diabetes compared with lean control participants. Future investigation is needed to explore potential treatment targets as identified by our study, including clock enhancement and induction of EIF2 signalling. DATA AVAILABILITY: The raw sequencing data and supplementary files for rhythmic expression analysis and Ingenuity Pathway Analysis have been deposited in NCBI Gene Expression Omnibus (GEO series accession number GSE104674).

Kinetics of phytoremediation of petroleum hydrocarbon contaminated soil.

Earthmaster and the University of Waterloo have successfully developed plant growth promoting rhizobacteria (PGPR) - Enhanced Phytoremediation Systems (PEPSystems™) which have been deployed across Canada for the treatment of soil contaminated with petroleum hydrocarbons (PHCs), including CCME fractions F2 and F3. A challenge with phytoremediation is to predict the length of time to remediate a site so that site owners will be inclined to use the technology. In previous field trials of PEPSystems, it was determined that PHC was mostly degraded by microbes in the rhizosphere, following first-order exponential decay kinetics. Using new PEPSystems data collected from multiple commercial remediation sites across Western Canada, the kinetic equations of PHC decay were tested to determine if remediation time was accurately predicted. In general, when compared to the predicted time to remediation endpoint, data from recent commercial field applications showed that 35% and 20% less time was needed to reach remediation endpoints for fractions F2 and F3, respectively. As a result, the predictive kinetic equation for fraction F2 degradation was updated to reflect current remediation outcomes. Insufficient data were available to update the F3 equation. Being able to more accurately predict remediation timelines will enhance the value and utilization of PEPSystems.

HepaRG-Progenitor Cell Derived Hepatocytes Cultured in Bioartificial Livers Are Protected from Healthy- and Acute Liver Failure-Plasma Induced Toxicity.

BACKGROUND/AIMS: For applicability of cell-based therapies aimed at the treatment of liver failure, such as bioartificial livers (BALs) and hepatocyte transplantation, it is essential that the applied hepatocytes tolerate exposure to the patient plasma. However, plasma from both healthy donors and acute liver failure (ALF) patients is detrimental to hepatocytes and hepatic cell lines, such as HepaRG. We aimed to elucidate the underlying mechanisms of plasma-induced toxicity against HepaRG cells in order to ultimately develop methods to reduce this toxicity and render HepaRG-BAL treatment more effective. METHODS: Differentiated HepaRG cells cultured in monolayers and laboratory-scale BALs were exposed to culture medium, healthy human plasma, healthy porcine plasma and ALF porcine plasma. Healthy human plasma was fractionated based on size- and polarity, albumin depleted and heat treated to characterize the toxic fraction. The cells were assessed for viability by total protein content and trypan blue staining. Their hepatic differentiation was assessed on transcript level through qRT-PCR and microarray analysis, and on functional level for Cytochrome P450 3A4 activity and ammonia elimination. Mitochondrial damage was assessed by JC-1 staining and mitochondrial gene transcription. RESULTS: Sixteen hours of healthy human plasma exposure did not affect viability, however, hepatic gene-transcript levels decreased dramatically and dose-dependently within four hours of exposure. These changes were associated with early NF-kB signaling and a shift from mitochondrial energy metabolism towards glycolysis. Healthy human plasma-toxicity was associated with the dose-dependent presence of heat-resistant, albumin-bound and (partly) hydrophobic toxic compound(s). HepaRG cells cultured in BALs were partially protected from plasma-toxicity, which was mainly attributable to medium perfusion and/or 3D configuration applied during BAL culturing. The detrimental human plasma effects were reversible in BAL-cultured cells. Porcine ALF-plasma elicited mitotoxicity additional to the basal detrimental effect of porcine healthy plasma, which were only partially reversible. CONCLUSION: A specific fraction of human plasma reduces hepatic differentiation of HepaRG cultures, in association with early NF-κB activation. In addition, ALF-plasma elicits mitotoxic effects. These findings allow for a targeted approach in preventing plasma-induced cell damage.

Study Design and qPCR Data Analysis Guidelines for Reliable Circulating miRNA Biomarker Experiments: A Review.

BACKGROUND: In the past decade, the search for circulating microRNA (miRNA) biomarkers has yielded numerous associations between miRNAs and different types of disease. However, many of these relations could not be replicated in subsequent studies under similar experimental conditions. Although this lack of replicability may be explained by the variation in experimental design and analysis methods, guidelines on the most appropriate design and analysis methods to study circulating miRNAs are scarce. CONTENT: miRNA biomarker experiments generally consist of a discovery phase and a validation phase. In the discovery phase, typically hundreds of miRNAs are measured in parallel to identify candidate biomarkers. Because of the costs of such high-throughput experiments, the number of individuals included in those studies is often too small, which can easily lead to false positives and false negatives. In the validation phase, a small number of identified biomarker candidates are measured in a large cohort of cases and controls, generally by quantitative PCR (qPCR). Although qPCR is a sensitive method to measure miRNAs in the circulation, experimental design and qPCR data analysis remain challenging. Omitting some crucial steps in the design and analysis of the qPCR experiment or performing them incorrectly can cause serious biases, ultimately leading to false conclusions. SUMMARY: In this review, we aim to expose and discuss the most common sources of interstudy variation in miRNA research from a methodological point of view and to provide guidelines on how to perform these steps correctly to increase replicability of studies on circulating miRNAs.

Bright nanowire single photon source based on SiV centers in diamond.

The practical implementation of many quantum technologies relies on the development of robust and bright single photon sources that operate at room temperature. The negatively charged silicon-vacancy (SiV-) color center in diamond is a possible candidate for such a single photon source. However, due to the high refraction index mismatch to air, color centers in diamond typically exhibit low photon out-coupling. An additional shortcoming is due to the random localization of native defects in the diamond sample. Here we demonstrate deterministic implantation of Si ions with high conversion efficiency to single SiV- centers, targeted to fabricated nanowires. The co-localization of single SiV- centers with the nanostructures yields a ten times higher light coupling efficiency than for single SiV- centers in bulk diamond. This enhanced photon out-coupling, together with the intrinsic scalability of the SiV- creation method, enables a new class of devices for integrated photonics and quantum science.

Multi-OMIC profiling of survival and metabolic signaling networks in cells subjected to photodynamic therapy.

Photodynamic therapy (PDT) is an established palliative treatment for perihilar cholangiocarcinoma that is clinically promising. However, tumors tend to regrow after PDT, which may result from the PDT-induced activation of survival pathways in sublethally afflicted tumor cells. In this study, tumor-comprising cells (i.e., vascular endothelial cells, macrophages, perihilar cholangiocarcinoma cells, and EGFR-overexpressing epidermoid cancer cells) were treated with the photosensitizer zinc phthalocyanine that was encapsulated in cationic liposomes (ZPCLs). The post-PDT survival pathways and metabolism were studied following sublethal (LC50) and supralethal (LC90) PDT. Sublethal PDT induced survival signaling in perihilar cholangiocarcinoma (SK-ChA-1) cells via mainly HIF-1-, NF-кB-, AP-1-, and heat shock factor (HSF)-mediated pathways. In contrast, supralethal PDT damage was associated with a dampened survival response. PDT-subjected SK-ChA-1 cells downregulated proteins associated with EGFR signaling, particularly at LC90. PDT also affected various components of glycolysis and the tricarboxylic acid cycle as well as metabolites involved in redox signaling. In conclusion, sublethal PDT activates multiple pathways in tumor-associated cell types that transcriptionally regulate cell survival, proliferation, energy metabolism, detoxification, inflammation/angiogenesis, and metastasis. Accordingly, tumor cells sublethally afflicted by PDT are a major therapeutic culprit. Our multi-omic analysis further unveiled multiple druggable targets for pharmacological co-intervention.

The dynamics of early-state transcriptional changes and aggregate formation in a Huntington's disease cell model.

BACKGROUND: Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a CAG expansion in the Huntingtin (HTT) gene. Proteolytic cleavage of mutant huntingtin (Htt) protein with an expanded polyglutamine (polyQ) stretch results in production of Htt fragments that aggregate and induce impaired ubiquitin proteasome, mitochondrial functioning and transcriptional dysregulation. To understand the time-resolved relationship between aggregate formation and transcriptional changes at early disease stages, we performed temporal transcriptome profiling and quantification of aggregate formation in living cells in an inducible HD cell model. RESULTS: Rat pheochromocytoma (PC12) cells containing a stably integrated, doxycycline-inducible, eGFP-tagged N-terminal human Htt fragment with an expanded polyQ domain were used to analyse gene expression changes at different stages of mutant Htt aggregation. At earliest time points after doxycycline induction no detectable aggregates and few changes in gene expression were observed. Aggregates started to appear at intermediate time points. Aggregate formation and subsequent enlargement of aggregates coincided with a rapid increase in the number of differentially expressed (DE) genes. The increase in number of large aggregates coincided with a decrease in the number of smaller aggregates whereas the transcription profile reverted towards the profile observed before mutant Htt induction. Cluster-based analysis of the 2,176 differentially expressed genes revealed fourteen distinct clusters responding differently over time. Functional enrichment analysis of the two major gene clusters revealed that genes in the up-regulated cluster were mainly involved in metabolic (antioxidant activity and cellular ketone metabolic processes) and genes in the down-regulated cluster in developmental processes, respectively. Promoter-based analysis of the identified gene clusters resulted in identification of a transcription factor network of which several previously have been linked to HD. CONCLUSIONS: We demonstrate a time-resolved relationship between Htt aggregation and changes in the transcriptional profile. We identified two major gene clusters showing involvement of (i) mitochondrial dysfunction and (ii) developmental processes implying cellular homeostasis defects. We identified novel and known HD-linked transcription factors and show their interaction with known and predicted regulatory proteins. Our data provide a novel resource for hypothesis building on the role of transcriptional key regulators in early stages of HD and possibly other polyQ-dependent diseases.

compendiumdb: an R package for retrieval and storage of functional genomics data.

UNLABELLED: Currently, the Gene Expression Omnibus (GEO) contains public data of over 1 million samples from more than 40 000 microarray-based functional genomics experiments. This provides a rich source of information for novel biological discoveries. However, unlocking this potential often requires retrieving and storing a large number of expression profiles from a wide range of different studies and platforms. The compendiumdb R package provides an environment for downloading functional genomics data from GEO, parsing the information into a local or remote database and interacting with the database using dedicated R functions, thus enabling seamless integration with other tools available in R/Bioconductor. AVAILABILITY AND IMPLEMENTATION: The compendiumdb package is written in R, MySQL and Perl. Source code and binaries are available from CRAN (http://cran.r-project.org/web/packages/compendiumdb/) for all major platforms (Linux, MS Windows and OS X) under the GPLv3 license. CONTACT: p.d.moerland@amc.uva.nl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.