Widespread and Functional RNA Circularization in Localized Prostate Cancer.

The cancer transcriptome is remarkably complex, including low-abundance transcripts, many not polyadenylated. To fully characterize the transcriptome of localized prostate cancer, we performed ultra-deep total RNA-seq on 144 tumors with rich clinical annotation. This revealed a linear transcriptomic subtype associated with the aggressive intraductal carcinoma sub-histology and a fusion profile that differentiates localized from metastatic disease. Analysis of back-splicing events showed widespread RNA circularization, with the average tumor expressing 7,232 circular RNAs (circRNAs). The degree of circRNA production was correlated to disease progression in multiple patient cohorts. Loss-of-function screening identified 11.3% of highly abundant circRNAs as essential for cell proliferation; for ∼90% of these, their parental linear transcripts were not essential. Individual circRNAs can have distinct functions, with circCSNK1G3 promoting cell growth by interacting with miR-181. These data advocate for adoption of ultra-deep RNA-seq without poly-A selection to interrogate both linear and circular transcriptomes.

Drought triggers and sustains overnight fires in North America.

Overnight fires are emerging in North America with previously unknown drivers and implications. This notable phenomenon challenges the traditional understanding of the 'active day, quiet night' model of the diurnal fire cycle1-3 and current fire management practices4,5. Here we demonstrate that drought conditions promote overnight burning, which is a key mechanism fostering large active fires. We examined the hourly diurnal cycle of 23,557 fires and identified 1,095 overnight burning events (OBEs, each defined as a night when a fire burned through the night) in North America during 2017-2020 using geostationary satellite data and terrestrial fire records. A total of 99% of OBEs were associated with large fires (>1,000 ha) and at least one OBE was identified in 20% of these large fires. OBEs were early onset after ignition and OBE frequency was positively correlated with fire size. Although warming is weakening the climatological barrier to night-time fires6, we found that the main driver of recent OBEs in large fires was the accumulated fuel dryness and availability (that is, drought conditions), which tended to lead to consecutive OBEs in a single wildfire for several days and even weeks. Critically, we show that daytime drought indicators can predict whether an OBE will occur the following night, which could facilitate early detection and management of night-time fires. We also observed increases in fire weather conditions conducive to OBEs over recent decades, suggesting an accelerated disruption of the diurnal fire cycle.

Renal nerve stimulation: complete versus incomplete renal sympathetic denervation.

PURPOSE: Blood pressure (BP) reduction after renal sympathetic denervation (RDN) is highly variable. Renal nerve stimulation (RNS) can localize sympathetic nerves. The RNS trial aimed to investigate the medium-term BP-lowering effects of the use of RNS during RDN, and explore if RNS can check the completeness of the denervation. MATERIAL AND METHODS: Forty-four treatment-resistant hypertensive patients were included in the prospective, single-center RNS trial. The primary study endpoint was change in 24-h BP at 6- to 12-month follow-up after RDN. The secondary study endpoints were the acute procedural RNS-induced BP response before and after RDN; number of antihypertensive drugs at follow-up; and the correlation between the RNS-induced BP increase before versus after RDN (delta [Δ] RNS-induced BP). RESULTS: Before RDN, the RNS-induced systolic BP rise was 43(±21) mmHg, and decreased to 9(±12) mmHg after RDN (p < 0.001). Mean 24-h systolic/diastolic BP decreased from 147(±12)/82(±11) mmHg at baseline to 135(±11)/76(±10) mmHg (p < 0.001/<0.001) at follow-up (10 [6-12] months), with 1 antihypertensive drug less compared to baseline. The Δ RNS-induced BP and the 24-h BP decrease at follow-up were correlated for systolic (R = 0.44, p = 0.004) and diastolic (R = 0.48, p = 0.003) BP. Patients with ≤0 mmHg residual RNS-induced BP response after RDN had a significant lower mean 24-h systolic BP at follow-up compared to the patients with >0 mmHg residual RNS-induced BP response (126 ± 4 mmHg versus 135 ± 10 mmHg, p = 0.04). 83% of the patients with ≤0 mmHg residual RNS-induced BP response had normal 24-h BP at follow-up, compared to 33% in the patients with >0 mmHg residual RNS-induced BP response (p = 0.023). CONCLUSION: The use of RNS during RDN leads to clinically significant and sustained lowering of 24-h BP with fewer antihypertensive drugs at follow-up. RNS-induced BP changes were correlated with 24-h BP changes at follow-up. Moreover, patients with complete denervation had significant lower BP compared to the patients with incomplete denervation.

Molecular characterization of colorectal adenomas reveals POFUT1 as a candidate driver of tumor progression.

Removal of colorectal adenomas is an effective strategy to reduce colorectal cancer (CRC) mortality rates. However, as only a minority of adenomas progress to cancer, such strategies may lead to overtreatment. The present study aimed to characterize adenomas by in-depth molecular profiling, to obtain insights into altered biology associated with the colorectal adenoma-to-carcinoma progression. We obtained low-coverage whole genome sequencing, RNA sequencing and tandem mass spectrometry data for 30 CRCs, 30 adenomas and 18 normal adjacent colon samples. These data were used for DNA copy number aberrations profiling, differential expression, gene set enrichment and gene-dosage effect analysis. Protein expression was independently validated by immunohistochemistry on tissue microarrays and in patient-derived colorectal adenoma organoids. Stroma percentage was determined by digital image analysis of tissue sections. Twenty-four out of 30 adenomas could be unambiguously classified as high risk (n = 9) or low risk (n = 15) of progressing to cancer, based on DNA copy number profiles. Biological processes more prevalent in high-risk than low-risk adenomas were related to proliferation, tumor microenvironment and Notch, Wnt, PI3K/AKT/mTOR and Hedgehog signaling, while metabolic processes and protein secretion were enriched in low-risk adenomas. DNA copy number driven gene-dosage effect in high-risk adenomas and cancers was observed for POFUT1, RPRD1B and EIF6. Increased POFUT1 expression in high-risk adenomas was validated in tissue samples and organoids. High POFUT1 expression was also associated with Notch signaling enrichment and with decreased goblet cells differentiation. In-depth molecular characterization of colorectal adenomas revealed POFUT1 and Notch signaling as potential drivers of tumor progression.

Consensus molecular subtype classification of colorectal adenomas.

Consensus molecular subtyping is an RNA expression-based classification system for colorectal cancer (CRC). Genomic alterations accumulate during CRC pathogenesis, including the premalignant adenoma stage, leading to changes in RNA expression. Only a minority of adenomas progress to malignancies, a transition that is associated with specific DNA copy number aberrations or microsatellite instability (MSI). We aimed to investigate whether colorectal adenomas can already be stratified into consensus molecular subtype (CMS) classes, and whether specific CMS classes are related to the presence of specific DNA copy number aberrations associated with progression to malignancy. RNA sequencing was performed on 62 adenomas and 59 CRCs. MSI status was determined with polymerase chain reaction-based methodology. DNA copy number was assessed by low-coverage DNA sequencing (n = 30) or array-comparative genomic hybridisation (n = 32). Adenomas were classified into CMS classes together with CRCs from the study cohort and from The Cancer Genome Atlas (n = 556), by use of the established CMS classifier. As a result, 54 of 62 (87%) adenomas were classified according to the CMS. The CMS3 'metabolic subtype', which was least common among CRCs, was most prevalent among adenomas (n = 45; 73%). One of the two adenomas showing MSI was classified as CMS1 (2%), the 'MSI immune' subtype. Eight adenomas (13%) were classified as the 'canonical' CMS2. No adenomas were classified as the 'mesenchymal' CMS4, consistent with the fact that adenomas lack invasion-associated stroma. The distribution of the CMS classes among adenomas was confirmed in an independent series. CMS3 was enriched with adenomas at low risk of progressing to CRC, whereas relatively more high-risk adenomas were observed in CMS2. We conclude that adenomas can be stratified into the CMS classes. Considering that CMS1 and CMS2 expression signatures may mark adenomas at increased risk of progression, the distribution of the CMS classes among adenomas is consistent with the proportion of adenomas expected to progress to CRC. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

An intensive multimodal group programme for patients with psychotic disorders at risk of rehospitalization: a controlled intervention study.

BACKGROUND: On the basis of earlier experiences in Germany and England, we developed an intensive multimodal group programme (FACT Plus) for psychotic-spectrum patients. By combining it with regular Flexible Assertive Community Treatment (FACT) (care as usual), we intended to reduce psychiatric rehospitalizations and mental healthcare costs. METHODS: We included adult patients (>18 years) with a psychotic spectrum disorder who had had at least one psychiatric admission in the 2 years before inclusion. FACT Plus was delivered weekly for 9 months. The intervention group was recruited in northern Rotterdam (the Netherlands), and the control group was recruited in southern Rotterdam. The primary outcome measure was length of stay (LOS) and the secondary outcome measures were mental healthcare costs and compulsory admissions. RESULTS: We included 52 patients in the intervention group and 61 patients in the control group. During the 12-month observation period, the mean LOS per patient was 15.2 (intervention group) and 34.6 (control group). This represents a difference of 19.4 days (56.1%). This result was statistically significant (B = -.859, SE = .497, p = .042) in a regression model correcting for baseline differences between the groups. Mean total mental healthcare costs per patient were €21,098 in the intervention group) versus €25,054 in the control group, a difference of about €4000 per patient (16%). In addition, there were zero compulsory admissions in the intervention group and nine in the control group. CONCLUSIONS: After the addition of FACT Plus to regular FACT, psychiatric LOS was substantially lower in the intervention group than in the control group. This result was accompanied by a limited reduction in mental healthcare costs.

Renal Nerve Stimulation as Procedural End Point for Renal Sympathetic Denervation.

PURPOSE OF REVIEW: Renal sympathetic denervation (RDN) as treatment option for hypertension has a strong rationale; however, variable effects on blood pressure (BP) have been reported ranging from non-response to marked reductions in BP. The absence of a procedural end point for RDN is one of the potential factors associated with the variable response. Studies have suggested the use of renal nerve stimulation (RNS) to adequately address this issue. This review aims to provide an overview of the clinical and experimental data available regarding the effects of RNS in the setting of RDN. RECENT FINDINGS: Animal studies have shown that high-frequency electrical stimulation of the sympathetic nerves in the adventitia of the renal arteries elicits an increase in BP and leads to an increased norepinephrine spillover as a marker of increased sympathetic activity and these effects of stimulation were attenuated or blunted after RDN. In a human feasibility study using RNS both before and after RDN, similar BP responses were observed. Moreover, in patients with resistant hypertension, RNS-induced changes in BP appeared to be correlated with 24-h BP response after RDN. These data suggest that RNS is a useful tool to identify renal sympathetic nerve fibers in patients with treatment-resistant hypertension undergoing RDN, and to predict the likely effectiveness of RDN treatments. In acute procedural settings both in animal and human models, RNS elicits increase in BP and HR before RDN and these effects are blunted after RDN. Up to now, there is preliminary evidence that the RNS-induced BP changes predict 24-h ABPM outcome at follow-up in patients with resistant hypertension. Of note, studies are small sized and results of large trials comparing conventional RDN to RNS-guided RDN are warranted.

Renal nerve stimulation identifies aorticorenal innervation and prevents inadvertent ablation of vagal nerves during renal denervation.

PURPOSE: Recently we reported the use of renal nerve stimulation (RNS) during renal denervation (RDN) procedures. RNS induced changes in blood pressure (BP) and heart rate are not fully delineated yet. We hypothesized that electrical stimulation of the sympathetic nerve tissue in the renal artery would lead to an increase in BP and vagal stimulation would cause a decrease in BP. We report the different patterns of BP and heart rate responses elicited by RNS prior to RDN. METHODS: 35 patients with drug-resistant hypertension were included. RNS was performed under general anesthesia at four sites in the right and left renal arteries, both before and immediately after RDN. RNS-induced BP and heart rate changes were monitored. RESULTS: A total of 289 RNS sites in 35 patients were analyzed. An increase in systolic BP of >10 mmHg was regarded as a positive BP response to RNS. This pattern of response was observed in 180 sites (62%). 86 RNS sites (30%) showed an indifferent response with BP changes ≤10 mmHg. At 13 sites (4.5%) RNS elicited a decrease in BP up to -8 mmHg. However, 10 RNS sites (3.5%) showed a pronounced vagal response with hypotension and sinus cycle lengths ranging between 4224-10272 milliseconds. These sites were distributed among two patients. CONCLUSION: RNS identified sympathetic and parasympathetic nerve tissue in the renal arteries. RNS can be potentially used to map nerve bundles and guide selective ablation of sympathetic nerve fibers and prevent inadvertent ablation of parasympathetic nerve tissue during RDN.

Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos.

BACKGROUND: Recently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time points at which pools of embryos are collected are usually still quite far apart. Here, we present a high-resolution gene-expression time series with 180 individual zebrafish embryos, obtained from nine different spawns, developmentally ordered and profiled from late blastula to mid-gastrula stage. On average one embryo per minute was analysed. The focus was on identification and description of the transcriptome dynamics of the expressed genes in this embryonic stage, rather than to biologically interpret profiles in cellular processes and pathways. RESULTS: In the late blastula to mid-gastrula stage, we found 6,734 genes being expressed with low variability and rather gradual changes. Ten types of dynamic behaviour were defined, such as genes with continuously increasing or decreasing expression, and all expressed genes were grouped into these types. Also, the exact expression starting and stopping points of several hundred genes during this developmental period could be pinpointed. Although the resolution of the experiment was so high, that we were able to clearly identify four known oscillating genes, no genes were observed with a peaking expression. Additionally, several genes showed expression at two or three distinct levels that strongly related to the spawn an embryo originated from. CONCLUSION: Our unique experimental set-up of whole-transcriptome analysis of 180 individual embryos, provided an unparalleled in-depth insight into the dynamics of early zebrafish embryogenesis. The existence of a tightly regulated embryonic transcriptome program, even between individuals from different spawns is shown. We have made the expression profile of all genes available for domain experts. The fact that we were able to separate the different spawns by their gene-expression variance over all expressed genes, underlines the importance of spawn specificity, as well as the unexpectedly tight gene-expression regulation in early zebrafish embryogenesis.

Crucial factors preceding compulsory psychiatric admission: a qualitative patient-record study.

BACKGROUND: Compulsory admissions have a strong effect on psychiatric patients and represent a deprivation of personal liberty. Although the rate of such admissions is tending to rise in several Western countries, there is little qualitative research on the mental health-care process preceding compulsory admission. The objective of the study was to identify crucial factors in the mental health-care process preceding compulsory admission of adult psychiatric patients. METHODS: This retrospective, qualitative multiple-case study was based on the patient records of patients with severe mental illness, mainly schizophrenia and other psychotic disorders. Twenty two patient records were analyzed. Patients' demographic and clinical characteristics were heterogeneous. All were treated by Flexible Assertive Community Treatment teams (FACT teams) at two mental health institutions in the greater Rotterdam area in the Netherlands and had a compulsory admission in a predefined inclusion period. The data were analyzed according to the Prevention and Recovery System for Monitoring and Analysis (PRISMA) method, assessing acts, events, conditions, and circumstances, failing protective barriers and protective recovery factors. RESULTS: The most important patient factors in the process preceding compulsory admission were psychosis, aggression, lack of insight, care avoidance, and unauthorized reduction or cessation of medication. Neither were health-care professionals as assertive as they could be in managing early signs of relapse and care avoidance of these particular patients. CONCLUSION: The health-care process preceding compulsory admission is complex, being influenced by acts, events, conditions and circumstances, failing barriers, and protective factors. The most crucial factors are patients' lack of insight and cessation of medication, and health-care professionals' lack of assertiveness.

A phase-space beam position monitor for synchrotron radiation.

The stability of the photon beam position on synchrotron beamlines is critical for most if not all synchrotron radiation experiments. The position of the beam at the experiment or optical element location is set by the position and angle of the electron beam source as it traverses the magnetic field of the bend-magnet or insertion device. Thus an ideal photon beam monitor would be able to simultaneously measure the photon beam's position and angle, and thus infer the electron beam's position in phase space. X-ray diffraction is commonly used to prepare monochromatic beams on X-ray beamlines usually in the form of a double-crystal monochromator. Diffraction couples the photon wavelength or energy to the incident angle on the lattice planes within the crystal. The beam from such a monochromator will contain a spread of energies due to the vertical divergence of the photon beam from the source. This range of energies can easily cover the absorption edge of a filter element such as iodine at 33.17 keV. A vertical profile measurement of the photon beam footprint with and without the filter can be used to determine the vertical centroid position and angle of the photon beam. In the measurements described here an imaging detector is used to measure these vertical profiles with an iodine filter that horizontally covers part of the monochromatic beam. The goal was to investigate the use of a combined monochromator, filter and detector as a phase-space beam position monitor. The system was tested for sensitivity to position and angle under a number of synchrotron operating conditions, such as normal operations and special operating modes where the photon beam is intentionally altered in position and angle at the source point. The results are comparable with other methods of beam position measurement and indicate that such a system is feasible in situations where part of the synchrotron beam can be used for the phase-space measurement.

Development of repeated sprint ability in talented youth basketball players.

Factors affecting repeated sprint ability (RSA) were evaluated in a mixed-longitudinal sample of 48 elite basketball players 14-19 years of age (16.1 ± 1.7 years). Players were observed on 6 occasions during the 2008-09 and 2009-10 seasons. Three following basketball-specific field tests were administered on each occasion: the shuttle sprint test for RSA, the vertical jump for lower body explosive strength (power), and the interval shuttle run test for interval endurance capacity. Height and weight were measured; body composition was estimated (percent fat, lean body mass). Multilevel modeling of RSA development curve was used with 32 players (16.0 ± 1.7 years) who had 2 or more observations. The 16 players (16.1 ± 1.8 years) measured on only 1 occasion were used as a control group to evaluate the appropriateness of the model. Age, lower body explosive strength, and interval endurance capacity significantly contributed to RSA (p ≤ 0.05). Repeated sprint ability improved with age from 14 to 17 years (p ≤ 0.05) and reached a plateau at 17-19 years. Predicted RSA did not significantly differ from measured RSA in the control group (p ≥ 0.05). The results suggest a potentially important role for the training of lower body explosive strength and interval endurance capacity in the development of RSA among youth basketball players. Age-specific reference values for RSA of youth players may assist basketball coaches in setting appropriate goals for individual players.

Landscape fires disproportionally affect high conservation value temperate peatlands, meadows, and deciduous forests, but only under low moisture conditions.

Landscape fires are a natural component of the Earth System. However, they are of growing global concern due to climate change exacerbating their multiple impacts on biodiversity, ecosystems, carbon storage, human health, economies, and wider society. Temperate regions are predicted to be at greatest risk of increasing fire activity due to climate change, where fires can seriously impact important ecosystems for biodiversity and carbon storage, such as peatlands and forests. There is insufficient literature on the background prevalence, distribution, and drivers of fires in these regions, especially within Europe, to assess and mitigate their risks. Using a global database of fire patches based on the MODIS FireCCI51 product, we address this knowledge gap by quantifying the current prevalence and size of fires in Polesia, a 150,000 km2 area comprising a mosaic of peatland, forest, and agricultural habitats in northern Ukraine and southern Belarus. Between 2001 and 2019, fires burned 31,062 km2 of land, and were most frequent in spring and autumn. Although most fires started in agricultural land, fires disproportionately affected natural and semi-natural land cover types, particularly in protected areas. Over one fifth of protected land burned. Coniferous forests were the most common land cover type in protected areas, but fires mostly occurred in meadows, open peatlands (especially fen and transition mires), and native deciduous forests. These land cover types were highly susceptible to fires under low soil moisture conditions, but the risk of fire was low under average or higher soil moisture conditions. Restoring and maintaining natural hydrological regimes could be an effective nature-based solution to increase the resilience of fire-vulnerable ecosystems and support global biodiversity and carbon storage commitments under the United Nations Framework Conventions on Climate Change and Convention on Biological Diversity.

Full characterization of RF compressed femtosecond electron pulses using ponderomotive scattering.

High bunch charge, femtosecond, electron pulses were generated using a 95 kV electron gun with an S-band RF rebunching cavity. Laser ponderomotive scattering in a counter-propagating beam geometry is shown to provide high sensitivity with the prerequisite spatial and temporal resolution to fully characterize, in situ, both the temporal profile of the electron pulses and RF time timing jitter. With the current beam parameters, we determined a temporal Instrument Response Function (IRF) of 430 fs FWHM. The overall performance of our system is illustrated through the high-quality diffraction data obtained for the measurement of the electron-phonon relaxation dynamics for Si (001).

Gene expression patterns and life cycle responses of toxicant-exposed chironomids.

Cellular stress responses are frequently presumed to be more sensitive than traditional ecotoxicological life cycle end points such as survival and growth. Yet, the focus to reduce test duration and to generate more sensitive end points has caused transcriptomics studies to be performed at low doses during short exposures, separately and independently from traditional ecotoxicity tests, making comparisons with life cycle end points indirect. Therefore we aimed to directly compare the effects on growth, survival, and gene expression of the nonbiting midge Chironomus riparius. To this purpose, we simultaneously analyzed life cycle and transcriptomics responses of chironomid larvae exposed to four model toxicants. We observed that already at the lowest test concentrations many transcripts were significantly differentially expressed, while the life cycle end points of C. riparius were hardly affected. Analysis of the differentially expressed transcripts showed that at the lowest test concentrations substantial and biologically relevant cellular stress was induced and that many transcripts responded already maximally at these lowest test concentrations. The direct comparison between molecular end life cycle responses after fourteen days of exposure revealed that gene expression is more sensitive to toxicant exposure than life cycle end points, underlining the potential of transcriptomics for ecotoxicity testing and environmental risk assessment.

The Impella 2.5 and 5.0 devices for ST-elevation myocardial infarction patients presenting with severe and profound cardiogenic shock: the Academic Medical Center intensive care unit experience.

OBJECTIVE: Cardiogenic shock remains an important therapeutic challenge, with high in-hospital mortality rates. Mechanical circulatory support may be beneficial in these patients. Since the efficacy of the intra-aortic balloon pump seems limited, new percutaneously placed mechanical left ventricular support devices, such as the Impella system, have been developed for this purpose. Our current purpose was to describe our experience with the Impella system in patients with ST-elevation myocardial infarction presenting in profound cardiogenic shock, who were admitted to our intensive care unit for mechanical ventilation. METHODS: From January 2004 through August 2010, a total of 34 ST-elevation myocardial infarction patients with profound cardiogenic shock were admitted to our intensive care unit and treated with either the Impella 2.5 or the Impella 5.0 device. Baseline and follow-up characteristics were collected retrospectively. MEASUREMENTS AND MAIN RESULTS: Within the study cohort, 25 patients initially received treatment with the Impella 2.5, whereas nine patients received immediate Impella 5.0 support. Eight out of 25 patients in the Impella 2.5 group were upgraded to 5.0 support. After 48 hrs, 14 of 25 patients in the 2.5 group were alive, five of whom had been upgraded. In the 5.0 group, eight out of nine patients were alive. After 30 days, six of 25 patients in the 2.5 group were alive, three of whom had been upgraded. In the 5.0 group, three of nine patients were alive at 30 days. CONCLUSIONS: In ST-elevation myocardial infarction patients with severe and profound cardiogenic shock, our initial experience suggests improved survival in patients who received immediate Impella 5.0 treatment, as well as in patients who were upgraded from 2.5 to 5.0 support, when compared to patients who received only Impella 2.5 support.

Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data.

BACKGROUND: Fusion genes are typically identified by RNA sequencing (RNA-seq) without elucidating the causal genomic breakpoints. However, non-poly(A)-enriched RNA-seq contains large proportions of intronic reads that also span genomic breakpoints. RESULTS: We have developed an algorithm, Dr. Disco, that searches for fusion transcripts by taking an entire reference genome into account as search space. This includes exons but also introns, intergenic regions, and sequences that do not meet splice junction motifs. Using 1,275 RNA-seq samples, we investigated to what extent genomic breakpoints can be extracted from RNA-seq data and their implications regarding poly(A)-enriched and ribosomal RNA-minus RNA-seq data. Comparison with whole-genome sequencing data revealed that most genomic breakpoints are not, or minimally, transcribed while, in contrast, the genomic breakpoints of all 32 TMPRSS2-ERG-positive tumours were present at RNA level. We also revealed tumours in which the ERG breakpoint was located before ERG, which co-existed with additional deletions and messenger RNA that incorporated intergenic cryptic exons. In breast cancer we identified rearrangement hot spots near CCND1 and in glioma near CDK4 and MDM2 and could directly associate this with increased expression. Furthermore, in all datasets we find fusions to intergenic regions, often spanning multiple cryptic exons that potentially encode neo-antigens. Thus, fusion transcripts other than classical gene-to-gene fusions are prominently present and can be identified using RNA-seq. CONCLUSION: By using the full potential of non-poly(A)-enriched RNA-seq data, sophisticated analysis can reliably identify expressed genomic breakpoints and their transcriptional effects.

The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis.

BACKGROUND: The Gram negative anaerobic bacterium Porphyromonas gingivalis has long been recognized as a causative agent of periodontitis. Periodontitis is a chronic infectious disease of the tooth supporting tissues eventually leading to tooth-loss. Capsular polysaccharide (CPS) of P. gingivalis has been shown to be an important virulence determinant. Seven capsular serotypes have been described. Here, we used micro-array based comparative genomic hybridization analysis (CGH) to analyze a representative of each of the capsular serotypes and a non-encapsulated strain against the highly virulent and sequenced W83 strain. We defined absent calls using Arabidopsis thaliana negative control probes, with the aim to distinguish between aberrations due to mutations and gene gain/loss. RESULTS: Our analyses allowed us to call aberrant genes, absent genes and divergent regions in each of the test strains. A conserved core P. gingivalis genome was described, which consists of 80% of the analyzed genes from the sequenced W83 strain. The percentage of aberrant genes between the test strains and control strain W83 was 8.2% to 13.7%. Among the aberrant genes many CPS biosynthesis genes were found. Most other virulence related genes could be found in the conserved core genome. Comparing highly virulent strains with less virulent strains indicates that hmuS, a putative CobN/Mg chelatase involved in heme uptake, may be a more relevant virulence determinant than previously expected. Furthermore, the description of the 39 W83-specific genes could give more insight in why this strain is more virulent than others. CONCLUSION: Analyses of the genetic content of the P. gingivalis capsular serotypes allowed the description of a P. gingivalis core genome. The high resolution data from three types of analysis of triplicate hybridization experiments may explain the higher divergence between P. gingivalis strains than previously recognized.

Photoacoustic spectroscopy using coherent synchrotron radiation: application to α-lactose monohydrate.

We produced coherent synchrotron radiation at the Canadian Light Source between about 5 and 30 cm(-1) in bursting and continuous emission modes and used it to acquire photoacoustic spectra of solids. A band was observed in the spectrum of α-lactose monohydrate at 18 cm(-1) and attributed to a rotational mode, in agreement with published data obtained using other numerical and experimental techniques.

Risk factors for repeated emergency compulsory psychiatric admissions.

BACKGROUND: The characteristics of patients who have repeated compulsory psychiatric admissions are largely unknown. AIMS: To investigate the frequency and risk factors for repeated emergency compulsory psychiatric admission (ECPA); and to identify targets for interventions to reduce repeated ECPA. METHOD: Data were collected from a database of electronic patient files (EPFs) held by three psychiatric emergency services (PES) in the Netherlands. Analyses were based on the data for adult patients (aged 18-75 years) with a first PES contact in 2010-2015. Using descriptive statistics and regression analysis, we studied the associations between baseline patient factors and repeated ECPA and time to readmission, within a 2-year follow-up period. RESULTS: We included 6059 patients: 15.6% had two or more ECPAs. In total, 66% of second ECPAs had occurred within 6 months of the first. About 30% of all ECPAs were repeated ECPAs. Two baseline factors were associated with a higher frequency of a second ECPA: history of receiving any mental healthcare treatment, whether in-patient or out-patient or both, and a lower level of self-care. Three were associated with a lower frequency: ethnicity (other than Dutch), older age and suicidality. Lower Global Assessment of Functioning (GAF) scores and housing problems were associated with a shorter time to compulsory readmission and persistent psychiatric problems with a longer time to compulsory readmission. CONCLUSIONS: We found that 15.6% of patients had two or more ECPAs. Two-thirds of the second ECPAs had occurred within 6 months of the first. Like earlier studies, the risk factors we identified suggest that interventions to reduce the risk of repeated compulsory psychiatric admission should seek to improve self-care, general daily functioning and homelessness.