Cerebral Oximetry Monitoring in Extremely Preterm Infants.

BACKGROUND: The use of cerebral oximetry monitoring in the care of extremely preterm infants is increasing. However, evidence that its use improves clinical outcomes is lacking. METHODS: In this randomized, phase 3 trial conducted at 70 sites in 17 countries, we assigned extremely preterm infants (gestational age, <28 weeks), within 6 hours after birth, to receive treatment guided by cerebral oximetry monitoring for the first 72 hours after birth or to receive usual care. The primary outcome was a composite of death or severe brain injury on cerebral ultrasonography at 36 weeks' postmenstrual age. Serious adverse events that were assessed were death, severe brain injury, bronchopulmonary dysplasia, retinopathy of prematurity, necrotizing enterocolitis, and late-onset sepsis. RESULTS: A total of 1601 infants underwent randomization and 1579 (98.6%) were evaluated for the primary outcome. At 36 weeks' postmenstrual age, death or severe brain injury had occurred in 272 of 772 infants (35.2%) in the cerebral oximetry group, as compared with 274 of 807 infants (34.0%) in the usual-care group (relative risk with cerebral oximetry, 1.03; 95% confidence interval, 0.90 to 1.18; P = 0.64). The incidence of serious adverse events did not differ between the two groups. CONCLUSIONS: In extremely preterm infants, treatment guided by cerebral oximetry monitoring for the first 72 hours after birth was not associated with a lower incidence of death or severe brain injury at 36 weeks' postmenstrual age than usual care. (Funded by the Elsass Foundation and others; SafeBoosC-III ClinicalTrials.gov number, NCT03770741.).

Haloperidol for the Treatment of Delirium in ICU Patients.

BACKGROUND: Haloperidol is frequently used to treat delirium in patients in the intensive care unit (ICU), but evidence of its effect is limited. METHODS: In this multicenter, blinded, placebo-controlled trial, we randomly assigned adult patients with delirium who had been admitted to the ICU for an acute condition to receive intravenous haloperidol (2.5 mg 3 times daily plus 2.5 mg as needed up to a total maximum daily dose of 20 mg) or placebo. Haloperidol or placebo was administered in the ICU for as long as delirium continued and as needed for recurrences. The primary outcome was the number of days alive and out of the hospital at 90 days after randomization. RESULTS: A total of 1000 patients underwent randomization; 510 were assigned to the haloperidol group and 490 to the placebo group. Among these patients, 987 (98.7%) were included in the final analyses (501 in the haloperidol group and 486 in the placebo group). Primary outcome data were available for 963 patients (97.6%). At 90 days, the mean number of days alive and out of the hospital was 35.8 (95% confidence interval [CI], 32.9 to 38.6) in the haloperidol group and 32.9 (95% CI, 29.9 to 35.8) in the placebo group, with an adjusted mean difference of 2.9 days (95% CI, -1.2 to 7.0) (P = 0.22). Mortality at 90 days was 36.3% in the haloperidol group and 43.3% in the placebo group (adjusted absolute difference, -6.9 percentage points [95% CI, -13.0 to -0.6]). Serious adverse reactions occurred in 11 patients in the haloperidol group and in 9 patients in the placebo group. CONCLUSIONS: Among patients in the ICU with delirium, treatment with haloperidol did not lead to a significantly greater number of days alive and out of the hospital at 90 days than placebo. (Funded by Innovation Fund Denmark and others; AID-ICU ClinicalTrials.gov number, NCT03392376; EudraCT number, 2017-003829-15.).

Open-source toolbox for photographic characterization of optical propagation.

An alternative method for characterizing optical propagation in waveguide structures based on scattered light imaging is presented and demonstrated for the spectral range of 450-980 nm. Propagation losses as low as 1.40 dB/cm are demonstrated in alumina spiral waveguides. AlGaAs-on-insulator waveguides are measured using a tunable laser and compared to cut-back measurements. On AlGaAs, a one-sigma uncertainty of 1.40 and 2.23 dB/cm for TE and TM polarizations is obtained for repetitions of measurements conducted on the same waveguide, highlighting the approach's reproducibility. An open-source toolbox is introduced, allowing for reliable processing of data and estimation of optical propagation losses.

Cerebral near-infrared spectroscopy monitoring (NIRS) in children and adults: a systematic review with meta-analysis.

BACKGROUND: Cerebral oxygenation monitoring utilising near-infrared spectroscopy (NIRS) is increasingly used to guide interventions in clinical care. The objective of this systematic review with meta-analysis and Trial Sequential Analysis is to evaluate the effects of clinical care with access to cerebral NIRS monitoring in children and adults versus care without. METHODS: This review conforms to PRISMA guidelines and was registered in PROSPERO (CRD42020202986). Methods are outlined in our protocol (doi: 10.1186/s13643-021-01660-2). RESULTS: Twenty-five randomised clinical trials were included (2606 participants). All trials were at a high risk of bias. Two trials assessed the effects of NIRS during neonatal intensive care, 13 during cardiac surgery, 9 during non-cardiac surgery and 1 during neurocritical care. Meta-analyses showed no significant difference for all-cause mortality (RR 0.75, 95% CI 0.51-1.10; 1489 participants; I2 = 0; 11 trials; very low certainty of evidence); moderate or severe, persistent cognitive or neurological deficit (RR 0.74, 95% CI 0.42-1.32; 1135 participants; I2 = 39.6; 9 trials; very low certainty of evidence); and serious adverse events (RR 0.82; 95% CI 0.67-1.01; 2132 participants; I2 = 68.4; 17 trials; very low certainty of evidence). CONCLUSION: The evidence on the effects of clinical care with access to cerebral NIRS monitoring is very uncertain. IMPACT: The evidence of the effects of cerebral NIRS versus no NIRS monitoring are very uncertain for mortality, neuroprotection, and serious adverse events. Additional trials to obtain sufficient information size, focusing on lowering bias risk, are required. The first attempt to systematically review randomised clinical trials with meta-analysis to evaluate the effects of cerebral NIRS monitoring by pooling data across various clinical settings. Despite pooling data across clinical settings, study interpretation was not substantially impacted by heterogeneity. We have insufficient evidence to support or reject the clinical use of cerebral NIRS monitoring.

Comparison of INVOS 5100C and Nonin SenSmart X-100 oximeter performance in preterm infants with spontaneous apnea.

BACKGROUND: Tissue oximeters are not interchangeable. Two instruments with sensors dedicated to preterm infants-INVOS 5100C and Nonin SenSmart X-100-have not yet been compared. METHODS: By measuring cerebral oxygenation in ten preterm infants with spontaneous apneic episodes defined by pulse oximeter readings (SpO2) below 80%, as well as tissue oxygenation during vascular occlusion on the forearm of ten adults, simultaneously we compared performance in the hypoxic range. RESULTS: We found the mean conversion equations to be StO2,SenSmart X-100 = 0.34 × StO2,INVOS 5100C + 44.8% during apnea in infants and StO2,SenSmart X-100 = 0.59 × StO2,INVOS 5100C + 34.4% during vascular occlusion. The individual regressions displayed large and statistically significant variations in both infants and adults. In three infants the INVOS sensor showed very little reaction to decreases in SpO2. CONCLUSIONS: These findings confirm that different NIRS devices give very different estimates when the oxygenation is low. The large variation when compared to SpO2 suggest that the sensor placement is very important in preterm infants.

Correction: Comparison of INVOS 5100C and Nonin SenSmart X-100 oximeter performance in preterm infants with spontaneous apnea.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

No neurodevelopmental benefit of cerebral oximetry in the first randomised trial (SafeBoosC II) in preterm infants during the first days of life.

AIM: Cerebral hypoxia has been associated with neurodevelopmental impairment. We studied whether reducing cerebral hypoxia in extremely preterm infants during the first 72 hours of life affected neurological outcomes at two years of corrected age. METHODS: In 2012-2013, the phase II randomised Safeguarding the Brains of our smallest Children trial compared visible cerebral near-infrared spectroscopy (NIRS) monitoring in an intervention group and blinded NIRS monitoring in a control group. Cerebral hypoxia was significantly reduced in the intervention group. We followed up 115 survivors from eight European centres at two years of corrected age, by conducting a medical examination and assessing their neurodevelopment with the Bayley Scales of Infant and Toddler Development, Second or Third Edition, and the parental Ages and Stages Questionnaire (ASQ). RESULTS: There were no differences between the intervention (n = 65) and control (n = 50) groups with regard to the mean mental developmental index (89.6 ± 19.5 versus 88.4 ± 14.7, p = 0.77), ASQ score (215 ± 58 versus 213 ± 58, p = 0.88) and the number of children with moderate-to-severe neurodevelopmental impairment (10 versus six, p = 0.58). CONCLUSION: Cerebral NIRS monitoring was not associated with long-term benefits or harm with regard to neurodevelopmental outcome at two years of corrected age.

Cerebral near-infrared spectroscopy monitoring for prevention of brain injury in very preterm infants.

BACKGROUND: Cerebral injury and long-term neurodevelopmental impairment is common in extremely preterm infants. Cerebral near-infrared spectroscopy (NIRS) enables continuous estimation of cerebral oxygenation. This diagnostic method coupled with appropriate interventions if NIRS is out of normal range (that is cerebral oxygenation within the 55% to 85% range) may offer benefits without causing more harms. Therefore, NIRS coupled with appropriate responses to abnormal findings on NIRS needs assessment in a systematic review of randomised clinical trials and quasi-randomised studies. OBJECTIVES: To evaluate the benefits and harms of interventions that attempt to alter cerebral oxygenation guided by cerebral NIRS monitoring in order to prevent cerebral injury, improve neurological outcome, and increase survival in preterm infants born more than 8 weeks preterm. SEARCH METHODS: We used the standard search strategy of the Cochrane Neonatal Review Group to search the Cochrane Central Register of Controlled Trials (CENTRAL 2016, Issue 8), MEDLINE via PubMed (1966 to 10 September 2016), Embase (1980 to 10 September 2016), and CINAHL (1982 to 10 September 2016). We also searched clinical trial databases, conference proceedings, and the reference lists of retrieved articles for randomised clinical trials and quasi-randomised studies. SELECTION CRITERIA: Randomised clinical trials and quasi-randomised clinical studies comparing continuous cerebral NIRS monitoring for at least 24 hours versus blinded NIRS or versus no NIRS monitoring. DATA COLLECTION AND ANALYSIS: Two review authors independently selected, assessed the quality of, and extracted data from the included trials and studies. If necessary, we contacted authors for further information. We conducted assessments of risks of bias; risks of design errors; and controlled the risks of random errors with Trial Sequential Analysis. We assessed the quality of the evidence with GRADE. MAIN RESULTS: One randomised clinical trial met inclusion criteria, including infants born more than 12 weeks preterm. The trial employed adequate methodologies and was assessed at low risk of bias. One hundred and sixty-six infants were randomised to start continuous cerebral NIRS monitoring less than 3 hours after birth until 72 hours after birth plus appropriate interventions if NIRS was out of normal range according to a guideline versus conventional monitoring with blinded NIRS. There was no effect of NIRS plus guideline of mortality until term-equivalent age (RR 0.50, 95% CI 0.29 to 1.00; one trial; 166 participants). There were no effects of NIRS plus guideline on intraventricular haemorrhages: all grades (RR 0.93, 95% CI 0.65 to 1.34; one trial; 166 participants); grade III/IV (RR 0.57, 95% CI 0.25 to 1.31; one trial; 166 participants); and cystic periventricular leukomalacia (which did not occur in either group). Likewise, there was no effect of NIRS plus guideline on the occurrence of a patent ductus arteriosus (RR 1.96, 95% CI 0.94 to 4.08; one trial; 166 participants); chronic lung disease (RR 1.27, 95% CI 0.94 to 1.50; one trial; 166 participants); necrotising enterocolitis (RR 0.83, 95% CI 0.33 to 1.94; one trial; 166 participants); and retinopathy of prematurity (RR 1.64, 95% CI 0.75 to 3.00; one trial; 166 participants). There were no serious adverse events in any of the intervention groups. NIRS plus guideline caused more skin marks from the NIRS sensor in the control group than in the experimental group (unadjusted RR 0.31, 95% CI 0.10 to 0.92; one trial; 166 participants). There are no data regarding neurodevelopmental outcome, renal impairment or air leaks.The quality of evidence for all comparisons discussed above was assessed as very low apart from all-cause mortality and adverse events: these were assessed as low and moderate, respectively. The validity of all comparisons is hampered by a small sample of randomised infants, risk of bias due to lack of blinding, and indirectness of outcomes. AUTHORS' CONCLUSIONS: The only eligible randomised clinical trial did not demonstrate any consistent effects of NIRS plus a guideline on the assessed clinical outcomes. The trial was, however, only powered to detect difference in cerebral oxygenation, not morbidities or mortality. Our systematic review did not reach sufficient power to prove or disprove effects on clinical outcomes. Further randomised clinical trials with low risks of bias and low risks of random errors are needed.

Brain injury in the international multicenter randomized SafeBoosC phase II feasibility trial: cranial ultrasound and magnetic resonance imaging assessments.

BACKGROUND: Abnormal cerebral perfusion during the first days of life in preterm infants is associated with higher grades of intraventricular hemorrhages and lower developmental score. In SafeBoosC II, we obtained a significant reduction of cerebral hypoxia by monitoring cerebral oxygenation in combination with a treatment guideline. Here, we describe (i) difference in brain injury between groups, (ii) feasibility of serial cranial ultrasound (cUS) and magnetic resonance imaging (MRI), (iii) local and central cUS assessment. METHODS: Hundred and sixty-six extremely preterm infants were included. cUS was scheduled for day 1, 4, 7, 14, and 35 and at term-equivalent age (TEA). cUS was assessed locally (unblinded) and centrally (blinded). MRI at TEA was assessed centrally (blinded). Brain injury classification: no, mild/moderate, or severe. RESULTS: Severe brain injury did not differ significantly between groups: cUS (experimental 10/80, control 18/77, P = 0.32) and MRI (5/46 vs. 3/38, P = 0.72). Kappa values for local and central readers were moderate-to-good for severe and poor-to-moderate for mild/moderate injuries. At TEA, cUS and MRI were assessed in 72 and 64%, respectively. CONCLUSION: There was no difference in severe brain injury between groups. Acquiring cUS and MRI according the standard operating procedures must be improved for future trials. Whether monitoring cerebral oxygenation during the first 72 h of life prevents brain injury should be evaluated in larger multicenter trials.

The SafeBoosC II randomized trial: treatment guided by near-infrared spectroscopy reduces cerebral hypoxia without changing early biomarkers of brain injury.

BACKGROUND: The SafeBoosC phase II multicentre randomized clinical trial investigated the benefits and harms of monitoring cerebral oxygenation by near-infrared spectroscopy (NIRS) combined with an evidence-based treatment guideline vs. no NIRS data and treatment as usual in the control group during the first 72 h of life. The trial demonstrated a significant reduction in the burden of cerebral hypoxia in the experimental group. We now report the blindly assessed and analyzed treatment effects on electroencephalographic (EEG) outcomes (burst rate and spectral edge frequency 95% (SEF95)) and blood biomarkers of brain injury (S100ß, brain fatty acid-binding protein, and neuroketal). METHODS: One hundred and sixty-six extremely preterm infants were randomized to either experimental or control group. EEG was recorded at 64 h of age and blood samples were collected at 6 and 64 h of age. RESULTS: One hundred and thirty-three EEGs were evaluated. The two groups did not differ regarding burst rates (experimental 7.2 vs. control 7.7 burst/min) or SEF95 (experimental 18.1 vs. control 18.0 Hz). The two groups did not differ regarding blood S100ß, brain fatty acid-binding protein, and neuroketal concentrations at 6 and 64 h (n = 123 participants). CONCLUSION: Treatment guided by NIRS reduced the cerebral burden of hypoxia without affecting EEG or the selected blood biomarkers.

Single-mode pumped high air-fill fraction photonic crystal fiber taper for high-power deep-blue supercontinuum sources.

Dispersion control with axially nonuniform photonic crystal fibers (PCFs) permits supercontinuum (SC) generation into the deep-blue from an ytterbium pump laser. In this Letter, we exploit the full degrees of freedom afforded by PCFs to fabricate a fiber with longitudinally increasing air-fill fraction and decreasing diameter directly on the draw-tower. We demonstrate SC generation extending down to 375 nm in one such monolithic fiber device that is single-mode at 1064 nm at the input end.

Sidestream dark field images of the microcirculation: intra-observer reliability and correlation between two semi-quantitative methods for determining flow.

BACKGROUND: Since analysis of Sidestream Dark Field images still requires subjective interpretation, we wanted to determine intra-observer repeatability and to estimate the correlation between different evaluation methods. METHODS: Fifty-four Sidestream Dark Field videos were analyzed twice by the same blinded observer using validated software. Vessels were detected, generating the parameter Total Vessel Density (TVD), and flow was determined by (i) classifying each vessel separately, generating the parameters Perfused Vessel Density (PVD) and Proportion of Perfused Vessels (PPV), and by (ii) the "Boerma" method, generating a Microvascular Flow Index (MFI) by quadrants. RESULTS: Intraclass Correlation Coefficients (ICCs) were above 0.9 for TVD and above 0.8 for PDV and PPV. MFIby quadrants had the lowest reliability (ICC = 0.52 for capillaries and ICC = 0.59 for all vessels), significantly lower than for PVD (ICC = 0.89, p < 0.001 for capillaries and ICC = 0.90, p < 0.001 for all vessels) and PPV (ICC = 0.82, p = 0.003 for capillaries and ICC = 0.83, p = 0.01 for all vessels). Correlation coefficient (r) between PPV and MFIby quadrants corrected for measurement error was 0.39 (0.10 - 0.64) for capillaries and 1.01 (0.85 - 1.16) for all vessels. CONCLUSIONS: Intra-observer reliability for full evaluation of Sidestream Dark Field images was good for vessel detection and for flow classification but significantly poorer for the faster "Boerma" method. Furthermore, the Boerma method is likely to estimate different aspects of capillary flow than do the standard methods.

Cerebral oxygenation after birth - a comparison of INVOS(®) and FORE-SIGHT™ near-infrared spectroscopy oximeters.

AIM: To compare absolute values of regional cerebral tissue oxygenation (cStO2 ) during haemodynamic transition after birth and repeatability during steady state for two commercial near-infrared spectroscopy (NIRS) devices. METHODS: In a prospective observational study, the INVOS 5100C and FORE-SIGHT were compared on 12 term newborns delivered by elective caesarean section. During the 10 min following umbilical cord clamping, cStO2 was measured simultaneously with the neonatal sensors from each device. Repeated measurements were taken the following day. RESULTS: Three and 8 min after clamping, the mean cStO2 value increased from 53.4% (CI 36.8-69.9%) to 86.0% (CI 80.2-91.7%) for INVOS and from 61.6% (CI 55.4-67.8%) to 82.2% (CI 77.7-86.7%) for FORE-SIGHT. The Bland-Altman plot revealed decreasing difference (INVOS minus FORE-SIGHT) (D) in absolute values (A) with increasing cStO2 (D = 0.5A - 38.19 p = <0.001). The mean steady-state value on day two was 78.4% (CI 74.6-82.2%) and 86.2% (CI 85.0-87.4%) for INVOS and FORE-SIGHT, respectively. The within-subject standard deviation during steady-state repeated measurements was 4.8% ± 0.86 for INVOS and 2.8% ± 0.5 for FORE-SIGHT. CONCLUSION: The INVOS and FORE-SIGHT cStO2 estimates showed oxygenation-level-dependent difference during birth transition. The better repeatability of FORE-SIGHT could be due to the lower response to change in saturation.

Peripheral tissue oximetry: comparing three commercial near-infrared spectroscopy oximeters on the forearm.

Estimation of regional tissue oxygenation (rStO2) by near infrared spectroscopy enables non-invasive end-organ oxygen balance monitoring and could be a valuable tool in intensive care. However, the diverse absolute values and dynamics of different devices, and overall poor repeatability of measurements are a problem. The aim of the present study is to test the hypothesis that INVOS 5100C, FORE-SIGHT and NONIN EQUANOX 7600 have similar properties concerning absolute values, repeatability, and sensitivity to changes in rStO2. To test repeatability the sensors were repositioned 20 times during hemodynamic steady state on the adult forearm. Afterwards six vascular occlusions by inflation of an upper arm cuff were done to achieve low oxygenation in the forearm. Absolute values were compared by repeated-measures ANOVA, repeatability was estimated by the within-subject standard deviation, Sw, and response to changing oxygenation by the down slope of rStO2 during vascular occlusion in the respective arm. 10 healthy adults, 21-29 years old, with double skinfolds on the forearm less than 10 mm participated. The median rStO2 was 70.7% (interquartile range (IQR) 7.7%), 68.4% (IQR 8.4%), and 64.6% (IQR 4.8) with INVOS, NONIN, and FORE-SIGHT, respectively, the median rate of decline was 13.2%/min (IQR 9.6), 22.8 %/min (IQR 18.0), and 10.8%/min (IQR 6.0), and the same-site repeatability was 2.9% (95% CI 2.4-3.3), 4.6% (CI 3.9-5.3), and 2.0% (CI 1.7-2.3). INVOS gave significantly higher steady state values than FORE-SIGHT, and NONIN had the steepest decline in rStO2, but the poorest repeatability. Two measures of signal-to-noise were similar among devices. This suggests that good repeatability comes at the expense of low sensitivity to changes in oxygenation. Values of rStO2 on the forearm from INVOS, NONIN and FORE-SIGTH cannot be used interchangeably.

Prospective Assessment of Fluorine-18-Fluorodeoxyglucose-Positron Emission Tomography/Computed Tomography (FDG-PET/CT) for Early Identification of Checkpoint-Inhibitor-Induced Pseudoprogression.

The activity of immune checkpoint inhibitors (ICIs) in patients with metastatic melanoma is often monitored using fluorine-18-fluorodeoxyglucose-positron emission tomography/computed tomography (FDG-PET/CT) scans. However, distinguishing disease progression (PD) from pseudoprogression (PsPD), where increased FDG uptake might reflect immune cell activity rather than tumor growth, remains a challenge. This prospective study compared the efficacy of dual-time point (DTP) FDG-PET/CT with modified response criteria (PERCIMT) in differentiating PsPD from PD. From July 2017-January 2021, 41 patients suspected to have PsPD on an evaluation scan were prospectively included (29 evaluable). A subsequent DTP FDG-PET/CT scan was conducted within 14 days, followed by a confirmatory FDG-PET/CT scan. Additionally, PERCIMT were applied. DTP FDG-PET/CT identified 24% with PsPD and 76% with PD. Applying PERCIMT criteria, 69% showed PsPD, while 31% had PD. On follow-up, 10 patients (34%) demonstrated confirmed PsPD, while 19 (66%) exhibited PD. The sensitivity and specificity of DTP FDG-PET/CT were 20% and 74%, respectively, and for PERCIMT this was 80% and 37%, respectively. Our findings suggest limited efficacy of DTP FDG-PET/CT in distinguishing PsPD from PD in ICI-treated patients with metastatic melanoma. The use of PERCIMT could complement clinical assessment and be incorporated in multidisciplinary team conferences for enhanced decision-making.

Miniature, multi-dichroic instrument for measuring the concentration of multiple fluorophores.

Identification of tumour margins during resection of the brain is critical for improving the post-operative outcomes. Due to the highly infiltrative nature of glioblastoma multiforme (GBM) and limited intraoperative visualization of the tumour margin, incomplete surgical resection has been observed to occur in up to 80 % of GBM cases, leading to nearly universal tumour recurrence and overall poor prognosis of 14.6 months median survival. This research presents a miniaturized, SiPMT-based optical system for simultaneous measurement of powerful DRS and weak auto-fluorescence for brain tumour detection. The miniaturisation of the optical elements confined the spatial separation of eight select wavelengths into footprint measuring 1.5 × 2 × 16 mm. The small footprint enables this technology to be integrated with existing surgical guidance instruments in the operating room. It's dynamic ability to subtract any background illumination and measure signal intensities across a broad range from pW to mWs make this design much more suitable for clinical environments as compared to spectrometer-based systems with limited dynamic ranges and high integration times. Measurements using optical tissue phantoms containing mixed fluorophores demonstrate correlation coefficients between the fitted response and actual concentration using PLS regression being 0.95, 0.87 and 0.97 for NADH, FAD and PpIX , respectively. These promising results indicate that our proposed miniaturized instrument could serve as an effective alternative in operating rooms, assisting surgeons in identifying brain tumours to achieving positive surgical outcomes for patients.

Sequence dependencies and mutation rates of localized mutational processes in cancer.

BACKGROUND: Cancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences. As a result, some sequence contexts mutate at much higher rates than others, with additional variation found between functional regions. Mutational hotspots, with recurrent mutations across cancer samples, represent genomic positions with elevated mutation rates, often caused by highly localized mutational processes. METHODS: We count the 11-mer genomic sequences across the genome, and using the PCAWG set of 2583 pan-cancer whole genomes, we associate 11-mers with mutational signatures, hotspots of single nucleotide variants, and specific genomic regions. We evaluate the mutation rates of individual and combined sets of 11-mers and derive mutational sequence motifs. RESULTS: We show that hotspots generally identify highly mutable sequence contexts. Using these, we show that some mutational signatures are enriched in hotspot sequence contexts, corresponding to well-defined sequence preferences for the underlying localized mutational processes. This includes signature 17b (of unknown etiology) and signatures 62 (POLE deficiency), 7a (UV), and 72 (linked to lymphomas). In some cases, the mutation rate and sequence preference increase further when focusing on certain genomic regions, such as signature 62 in transcribed regions, where the mutation rate is increased up to 9-folds over cancer type and mutational signature average. CONCLUSIONS: We summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates.

Pan-cancer association of DNA repair deficiencies with whole-genome mutational patterns.

DNA repair deficiencies in cancers may result in characteristic mutational patterns, as exemplified by deficiency of BRCA1/2 and efficacy prediction for PARP inhibitors. We trained and evaluated predictive models for loss-of-function (LOF) of 145 individual DNA damage response genes based on genome-wide mutational patterns, including structural variants, indels, and base-substitution signatures. We identified 24 genes whose deficiency could be predicted with good accuracy, including expected mutational patterns for BRCA1/2, MSH3/6, TP53, and CDK12 LOF variants. CDK12 is associated with tandem duplications, and we here demonstrate that this association can accurately predict gene deficiency in prostate cancers (area under the receiver operator characteristic curve = 0.97). Our novel associations include mono- or biallelic LOF variants of ATRX, IDH1, HERC2, CDKN2A, PTEN, and SMARCA4, and our systematic approach yielded a catalogue of predictive models, which may provide targets for further research and development of treatment, and potentially help guide therapy.

Many different aspects of the environment ­ such as ultraviolet radiation, carcinogens in food and drink, and the ageing process itself ­ damage the DNA in human cells. Normally, cells can repair these sites by activating a mechanism known as the DNA damage response. However, the hundreds of genes that orchestrate this response are also themselves often lost or damaged, allowing the unrepaired sites to turn into permanent mutations that accumulate across the genome of the cancer cell. By studying the DNA of cancer cells, it has been possible to identify characteristic patterns of mutations, called mutational signatures, that appear in different types of cancer. One specific pattern has been linked to the loss of either the BRCA1 or BRCA2 gene, both of which are part of the DNA damage response. However, it remained unclear how many other genes involved in the DNA damage response also lead to detectable mutational signatures when lost. To investigate, Sørensen et al. computationally analysed data from over six thousand cancer patients. They looked for associations between over 700 DNA damage response genes and 80 different mutational signatures. As expected, the analysis revealed a strong connection between the loss of BRCA1/BRCA2 and their known mutational signature. However, it also found 23 other associations between DNA damage response genes that had been lost or damaged and particular patterns of mutations in a variety of cancers. These findings suggest that mutational signatures could be used more widely to predict which DNA damage response genes are no longer functioning in the genome of cancer cells. The mutational signature caused by the loss of BRAC1/BRAC2 has been shown to make patients more responsive to a certain type of chemotherapy. Further experiments are needed to determine whether the connections identified by Sørensen et al. could also provide information on which treatment would benefit a cancer patient the most. In the future, this might help medical practitioners provide more personalized treatment.

Microcamera Visualisation System to Overcome Specular Reflections for Tissue Imaging.

In vivo tissue imaging is an essential tool for medical diagnosis, surgical guidance, and treatment. However, specular reflections caused by glossy tissue surfaces can significantly degrade image quality and hinder the accuracy of imaging systems. In this work, we further the miniaturisation of specular reflection reduction techniques using micro cameras, which have the potential to act as intra-operative supportive tools for clinicians. In order to remove these specular reflections, two small form factor camera probes, handheld at 10 mm footprint and miniaturisable to 2.3 mm, are developed using different modalities, with line-of-sight to further miniaturisation. (1) The sample is illuminated via multi-flash technique from four different positions, causing a shift in reflections which are then filtered out in a post-processing image reconstruction step. (2) The cross-polarisation technique integrates orthogonal polarisers onto the tip of the illumination fibres and camera, respectively, to filter out the polarisation maintaining reflections. These form part of a portable imaging system that is capable of rapid image acquisition using different illumination wavelengths, and employs techniques that lend themselves well to further footprint reduction. We demonstrate the efficacy of the proposed system with validating experiments on tissue-mimicking phantoms with high surface reflection, as well as on excised human breast tissue. We show that both methods can provide clear and detailed images of tissue structures along with the effective removal of distortion or artefacts caused by specular reflections. Our results suggest that the proposed system can improve the image quality of miniature in vivo tissue imaging systems and reveal underlying feature information at depth, for both human and machine observers, leading to better diagnosis and treatment outcomes.

Contemporary trends in the surgical management of urinary incontinence after radical prostatectomy in the United States.

PURPOSE: To identify trends, costs, and predictors in the use of different surgical procedures for post-radical prostatectomy incontinence (PPI). MATERIALS AND METHODS: We identified 21,589 men who were diagnosed with localized prostate cancer (PCa) and treated with radical prostatectomy (RP) from 2003 to 2017. The primary outcome was the incontinence procedure performances. Optum's de-identified Clinformatics® Data Mart Database was queried to define the cohort of interest. The average costs of the different incontinence procedures were obtained and compared. Also, demographic, and clinical predictors of incontinence surgery were evaluated by multivariable regression analysis. RESULTS: Of the 21,589 men with localized PCa treated with RP, 740 (3.43%) underwent at least one incontinence procedure during a median of 5 years of follow-up. In total, there were 844 unique incontinence procedures. Male slings were the most common procedure (47.5%), had an intermediate cost compared to the other treatment options, and was the first-choice treatment for the majority of patients (50%). The use of an artificial urinary sphincter (AUS) was the second most common (35.3%), but also was the most expensive treatment and was first-choice-treatment for 32.3% of patients. On multivariable analysis, metabolic syndrome related disorders, adjuvant/salvage radiation therapy as well as a history of neurological comorbidities were independently associated with an increased likelihood of incontinence surgery. CONCLUSIONS: The receipt of male slings increased and then subsequently decreased, while AUS utilization was stable, and the use of urethral bulking agents was uncommon. From a cost standpoint, AUS was the most expensive option. Finally, patient's comorbidity history and RP related factors were found to influence the choice for primary or subsequent PPI interventions.