Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.

Prediction of transcription factors associated with DNA demethylation during human cellular development.

DNA methylation of CpG dinucleotides is an important epigenetic modification involved in the regulation of mammalian gene expression, with each type of cell developing a specific methylation profile during its differentiation. Recently, it has been shown that a small subgroup of transcription factors (TFs) might promote DNA demethylation at their binding sites. We developed a bioinformatics pipeline to predict from genome-wide DNA methylation data TFs that promote DNA demethylation at their binding site. We applied the pipeline to International Human Epigenome Consortium methylome data and selected 393 candidate transcription factor binding motifs and associated 383 TFs that are likely associated with DNA demethylation. Validation of a subset of the candidate TFs using an in vitro assay suggested that 28 of 49 TFs from various TF families had DNA-demethylation-promoting activity; TF families, such as bHLH and ETS, contained both TFs with and without the activity. The identified TFs showed large demethylated/methylated CpG ratios and their demethylated CpGs showed significant bias toward hypermethylation in original cells. Furthermore, the identified TFs promoted demethylation of distinct sets of CpGs, with slight overlap of the targeted CpGs among TF family members, which was consistent with the results of a gene ontology (GO) term analysis of the identified TFs. Gene expression analysis of the identified TFs revealed that multiple TFs from various families are specifically expressed in human cells and tissues. Together, our results suggest that a large number of TFs from various TF families are associated with cell-type-specific DNA demethylation during human cellular development.

Performance of portable objective wound assessment tools: a systematic review.

OBJECTIVE: Accurate wound assessment is crucial for determining the progression of healing and guides treatment strategies. Portable wound assessment devices can be useful in providing an accurate evaluation in the community where most cases are treated. The objective of this review was to compare the performance of various portable wound assessment techniques used for wound healing assessment described in the literature. METHOD: In April 2020, electronic databases were searched, using appropriate search terms, for all available publications on the use of portable wound assessment devices on human and artificial wounds. The primary outcome was the reliability and reproducibility of measurement while the secondary outcome was the feasibility of the instrument. All studies underwent quality assessment of diagnostic accuracy studies (QUADAS) to examine the quality of data. RESULTS: A total of 129 articles were identified and 24 were included in the final review; 17 articles discussed two-dimensional (2D) devices; three articles discussed three-dimensional (3D) devices; and four articles discussed application-based devices. Most studies (n=8) reported on a 2D device that had an ICC of 0.92-0.99 for area measurement and a coefficient of variance of 3.1% with an error of 2.3% in human wounds and 1.55-3.7% in artificial wounds. The inter/intra observer reliability was 0.998 and 0.985, respectively with a scan time of two minutes per wound. The median QUADAS score was 12. CONCLUSION: Based on the presented evidence, 2D-based portable wound assessment devices were the most studied and demonstrated good performance. Further studies are required for 3D and application-based measurement instruments.

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.

In multicellular organisms, transcription regulation is one of the central mechanisms modelling lineage differentiation and cell-fate determination. Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements. It is believed that their communication occurs within large discrete foci of aggregated RNA polymerases termed transcription factories in three-dimensional nuclear space. However, the dynamic nature of chromatin connectivity has not been characterized at the genome-wide level. Here, through a chromatin interaction analysis with paired-end tagging approach using an antibody that primarily recognizes the pre-initiation complexes of RNA polymerase II, we explore the transcriptional interactomes of three mouse cells of progressive lineage commitment, including pluripotent embryonic stem cells, neural stem cells and neurosphere stem/progenitor cells. Our global chromatin connectivity maps reveal approximately 40,000 long-range interactions, suggest precise enhancer-promoter associations and delineate cell-type-specific chromatin structures. Analysis of the complex regulatory repertoire shows that there are extensive colocalizations among promoters and distal-acting enhancers. Most of the enhancers associate with promoters located beyond their nearest active genes, indicating that the linear juxtaposition is not the only guiding principle driving enhancer target selection. Although promoter-enhancer interactions exhibit high cell-type specificity, promoters involved in interactions are found to be generally common and mostly active among different cells. Chromatin connectivity networks reveal that the pivotal genes of reprogramming functions are transcribed within physical proximity to each other in embryonic stem cells, linking chromatin architecture to coordinated gene expression. Our study sets the stage for the full-scale dissection of spatial and temporal genome structures and their roles in orchestrating development.

Potato late blight field resistance from QTL dPI09c is conferred by the NB-LRR gene R8.

Following the often short-lived protection that major nucleotide binding, leucine-rich-repeat (NB-LRR) resistance genes offer against the potato pathogen Phytophthora infestans, field resistance was thought to provide a more durable alternative to prevent late blight disease. We previously identified the QTL dPI09c on potato chromosome 9 as a more durable field resistance source against late blight. Here, the resistance QTL was fine-mapped to a 186 kb region. The interval corresponds to a larger, 389 kb, genomic region in the potato reference genome of Solanum tuberosum Group Phureja doubled monoploid clone DM1-3 (DM) and from which functional NB-LRRs R8, R9a, Rpi-moc1, and Rpi_vnt1 have arisen independently in wild species. dRenSeq analysis of parental clones alongside resistant and susceptible bulks of the segregating population B3C1HP showed full sequence representation of R8. This was independently validated using long-range PCR and screening of a bespoke bacterial artificial chromosome library. The latter enabled a comparative analysis of the sequence variation in this locus in diverse Solanaceae. We reveal for the first time that broad spectrum and durable field resistance against P. infestans is conferred by the NB-LRR gene R8, which is thought to provide narrow spectrum race-specific resistance.

Association of CYP2C19*2 and associated haplotypes with lower norendoxifen concentrations in tamoxifen-treated Asian breast cancer patients.

AIM: The aim was to examine the influence of CYP2C19 variants and associated haplotypes on the disposition of tamoxifen and its metabolites, particularly norendoxifen (NorEND), in Asian patients with breast cancer. METHODS: Sixty-six CYP2C19 polymorphisms were identified in healthy Asians (n = 240), of which 14 were found to be tightly linked with CYP2C19*2, CYP2C19*3 and CYP2C19*17. These 17 SNPs were further genotyped in Asian breast cancer patients receiving tamoxifen (n = 201). Steady-state concentrations of tamoxifen and its metabolites were quantified using liquid chromatography­mass spectrometry. Non-parametric tests and regression methods were implemented to evaluate genotypic­phenotypic associations and haplotypic effects of the SNPs. RESULTS: CYP2C19 functional polymorphisms and their linked SNPs were not significantly associated with plasma concentrations of tamoxifen and its main metabolites N-desmethyltamoxifen, (Z)-4-hydroxytamoxifen and (Z)-Endoxifen. However, CYP2C19*2 and its seven linked SNPs were significantly associated with lower NorEND concentrations, MRNorEND/NDDM and MRNorEND/(Z)-END. Specifically, patients carrying the CYP2C19*2 variant allele A had significantly lower NorEND concentrations [median (range), GG vs. GA vs. AA: 1.51 (0.38­3.28) vs. 1.28 (0.30­3.36) vs. 1.15 ng ml−1 (0.26­2.45, P = 0.010)] as well as significantly lower MRNorEND/(Z)-END [GG vs. GA vs. AA: 9.40 (3.27­28.35) vs. 8.15 (2.67­18.9) vs. 6.06 (4.47­14.6), P < 0.0001] and MRNorEND/NDDM [GG vs. GA vs. AA: 2.75 (0.62­6.26) vs. 2.43 (0.96­4.18) vs. 1.75 (1.10­2.49), P < 0.00001]. CYP2C19 H2 haplotype, which included CYP2C19*2, was also significantly associated with lower NorEND concentrations (P = 0.0020), MRNorEND/NDDM (P < 0.0001) and MRNorEND/(Z)-END (P < 0.0001), indicating significantly lower formation rates of NorEND. CONCLUSION: These data highlight the potential relevance of CYP2C19 pharmacogenetics in influencing NorEND concentrations in tamoxifen-treated patients, which may influence treatment outcomes.

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community.

BACKGROUND: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composition and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for large initial DNA template quantities during library preparation. RESULTS: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition. CONCLUSIONS: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.

Assessing the incremental value of blood oxygen saturation (SpO(2)) in the miniPIERS (Pre-eclampsia Integrated Estimate of RiSk) Risk Prediction Model.

OBJECTIVE: To assess the incremental value of blood oxygen saturation (SpO(2)) as a predictor in the miniPIERS model, a risk prediction model for adverse outcomes among women with a diagnosis of hypertensive disorder of pregnancy (HDP) in low-resourced settings. METHODS: Using data from a prospective cohort including 852 women admitted to hospital for a HDP, the association between SpO(2) and adverse maternal outcome was assessed using logistic regression. The miniPIERS model was recalibrated and extended to include SpO(2). The incremental value of adding SpO(2) to the model was measured using a net reclassification index (NRI), sensitivity, specificity, positive and negative predictive values, and likelihood ratios. RESULTS: SpO(2) of < 93% was associated with a 30-fold increase in risk (95% CI 14 to 68) of adverse maternal outcome compared to women with SpO(2) > 97%. After recalibration and extension, the miniPIERS model including SpO(2) (vs. not including SpO(2)) had improved sensitivity (32.8% vs. 49.6%) at the cost of minimally decreased specificity (91.5% vs. 96.2%) with a NRI of 0.122. CONCLUSION: SpO(2) is a significant independent predictor of risk in women with a HDP. Adding SpO(2) to the miniPIERS model improved the model's ability to correctly identify high-risk patients who would benefit most from interventions.

Objectif : Évaluer la valeur cumulative de la saturation en oxygène (SaO2) à titre de facteur prédictif dans le cadre du modèle miniPIERS, soit un modèle de prévision des risques en ce qui concerne les issues indésirables chez les femmes ayant obtenu un diagnostic de trouble hypertensif de la grossesse (THG) dans des milieux qui ne disposent que de faibles ressources. Méthodes : Grâce à des données issues d'une cohorte prospective ayant porté sur 852 femmes hospitalisées en raison d'un THG, l'association entre la SaO2 et les issues indésirables maternelles a été évaluée au moyen d'une régression logistique. Le modèle miniPIERS a été recalibré et élargi de façon à inclure la SaO2. La valeur cumulative de l'ajout de la SaO2 à ce modèle a été mesurée en ayant recours à l'indice NRI (net reclassification index), à la sensibilité, à la spécificité, aux coefficients de prévision d'un test positif et d'un test négatif et aux rapports de vraisemblance. Résultats : La SaO2 < 93 % a été associée à un risque 30 fois plus élevé (IC à 95 %, 14 - 68) de constater une issue maternelle indésirable, par comparaison avec une SaO2 > 97 %. Après avoir été recalibré et élargi, le modèle miniPIERS comprenant la SaO2 (par comparaison avec le modèle ne comprenant pas la SaO2) présentait une sensibilité améliorée (32,8 % vs 49,6 %); cela a toutefois mené à une baisse minime de la spécificité (91,5 % vs 96,2 %) en présence d'un indice NRI de 0,122. Conclusion : La SaO2 constitue un facteur prédictif indépendant significatif pour ce qui est du risque auquel sont exposées les femmes qui présentent un THG. L'ajout de la SaO2 au modèle miniPIERS a mené à l'amélioration de la capacité de ce dernier à identifier correctement les patientes exposées à des risques élevés qui tireraient le plus avantage de la tenue d'interventions.

Radio-responsive tumors exhibit greater intratumoral immune activity than nonresponsive tumors.

Radiation therapy (RT) continues to be a cornerstone in the treatment for many cancers. Unfortunately, not all individuals respond effectively to RT resulting clinically in two groups consisting of nonresponders (progressive disease) and responders (tumor control/cure). The mechanisms that govern the outcome of radiotherapy are poorly understood. Interestingly, a new paradigm has emerged demonstrating that the immune system mediates many of the antitumor effects of RT. Therefore, we hypothesized that the immune response following RT may dictate the efficacy of treatment. To examine this, we developed a tumor model that mirrors this clinically relevant phenomenon in which mice bearing Colon38, a colon adenocarcinoma, were treated locally with 15Gy RT resulting in both nonresponders and responders. More importantly, we were able to distinguish responders from nonresponders as early as 4 days post-RT allowing for the unique opportunity to identify critical events that ultimately determined the effectiveness of therapy. Intratumoral immune cells and interferon-gamma were increased in responsive tumors and licensed CD8 T cells to exhibit lytic activity against tumor cells, a response that was diminished in tumors refractory to RT. Combinatorial treatment with RT and the immunomodulatory cytokine IL-12 resulted in complete remission of cancer in 100% of cases compared to a cure rate of only 12% with RT alone. Similar data were obtained when IL-12 was delivered by microspheres. Therefore, the efficacy of RT may depend on the strength of the immune response induced after radiotherapy. Additionally, immunotherapy that further stimulates the immune cells may enhance the effectiveness of RT.

Type I interferons induced by radiation therapy mediate recruitment and effector function of CD8(+) T cells.

The need for an intact immune system for cancer radiation therapy to be effective suggests that radiation not only acts directly on the tumor but also indirectly, through the activation of host immune components. Recent studies demonstrated that endogenous type I interferons (type I IFNs) play a role in radiation-mediated anti-tumor immunity by enhancing the ability of dendritic cells to cross-prime CD8(+) T cells. However, it is still unclear to what extent endogenous type I IFNs contribute to the recruitment and function of CD8(+) T cells. Little is also known about the effects of type I IFNs on myeloid cells. In the current study, we demonstrate that type I and type II IFNs (IFN-γ) are both required for the increased production of CXCL10 (IP-10) chemokine by myeloid cells within the tumor after radiation treatment. Radiation-induced intratumoral IP-10 levels in turn correlate with tumor-infiltrating CD8(+) T cell numbers. Moreover, type I IFNs promote potent tumor-reactive CD8(+) T cells by directly affecting the phenotype, effector molecule production, and enhancing cytolytic activity. Using a unique inducible expression system to increase local levels of IFN-α exogenously, we show here that the capacity of radiation therapy to result in tumor control can be enhanced. Our preclinical approach to study the effects of local increase in IFN-α levels can be used to further optimize the combination therapy strategy in terms of dosing and scheduling, which may lead to better clinical outcome.

Development of high-content gemcitabine PEGylated liposomes and their cytotoxicity on drug-resistant pancreatic tumour cells.

PURPOSE: The objective of this study was to develop high-content gemcitabine PEGylated liposomes to reverse gemcitabine resistance in pancreatic tumour cells. The mechanism of drug loading into liposomes was also investigated. METHODS: To increase the drug entrapment efficiency (EE) and drug loading (DL), a novel passive loading approach named Small Volume Incubation method (SVI) was developed and compared to the reverse phase evaporation (REV) and remote loading methods. The in vitro cytotoxicity was evaluated using MIA PaCa-2 and Panc-1 cell lines. RESULTS: The EE for remote loading was 12.3 ± 0.3%, much lower than expected and a burst release was observed with the resultant liposomes. Using the optimized SVI method, increased EE (37 ± 1%) and DL (4%, w/w) were obtained. The liposomes (200 ± 5 nm) showed minimal drug leakage, good stability, and significant improvement in cytotoxicity to the gemcitabine-resistant pancreatic cancer cell lines. CONCLUSIONS: Remote loading was not suitable for loading gemcitabine into liposomes. pKa > 4.6 for basic drugs and intra-liposomal precipitation of loaded compounds were suggested as an additional requirement to the current criteria for remote loading using ammonium sulphate gradient (pKa < 11). High DL is essential for liposomes to reverse gemcitabine resistance in pancreatic cell lines.

Pharmacogenetic effects of regulatory nuclear receptors (PXR, CAR, RXRα and HNF4α) on docetaxel disposition in Chinese nasopharyngeal cancer patients.

PURPOSE: This exploratory study was aimed at elucidating the pharmacogenetics of regulatory nuclear receptors (PXR, CAR, RXRα and HNF4α) and their implications on docetaxel pharmacokinetics and pharmacodynamics in local Chinese nasopharyngeal cancer patients. METHODS: A total of 59 single nucleotide polymorphisms (SNPs), including tag-SNPs and functionally relevant SNPs of the genes encoding these regulatory nuclear receptors (PXR/NR1I2, CAR/NR1I3, RXRα/NR2B1 and HNF4α/NR2A1), were profiled in the patients enrolled in our study by direct sequencing (N = 50). The generalized linear model was employed to estimate the haplotypic effects on the pharmacokinetics and pharmacodynamics of the patients. RESULTS: The pharmacokinetic profiles of docetaxel in these patients were characterized by marked interindividual variability, with approximately four- to sixfold variations observed in Cmax, AUC0-∞ and CL. Individual SNP association tests revealed that polymorphisms in NR2B1 and NR2A1 were significantly correlated with altered docetaxel pharmacokinetics. Subsequent haplotype association analysis identified the NR2B1 LD block 2 AG haplotype [*+4458G>A(rs3132291) and *+4988A>G(rs4842198)] to be significantly associated with altered pharmacokinetics, in which patients carrying two copies of the AG haplotype had approximately a 20 % decreased Cmax and AUC0-∞ and a 21 % increased CL compared to those who carried only one copy or no copies of the haplotype. A number of SNPs in NR1I2, NR1I3, NR2B1 and NR2A1 were also associated with a significant decrease in blood counts from baseline. No haplotype was found to exert any effects on the pharmacodynamics parameters. CONCLUSIONS: The present exploratory study identified several SNPs in the genes encoding regulatory nuclear receptors which may account for the interpatient variability in docetaxel pharmacokinetics and pharmacodynamics. These findings highlight the important role of regulatory nuclear receptors on the disposition of docetaxel.

Late Holocene relative sea-level records from coral microatolls in Singapore.

Late Holocene relative sea-level (RSL) data are important to understand the drivers of RSL change, but there is a lack of precise RSL records from the Sunda Shelf. Here, we produced a Late Holocene RSL reconstruction from coral microatolls in Singapore, demonstrating for the first time the utility of Diploastrea heliopora microatolls as sea-level indicators. We produced 12 sea-level index points and three marine limiting data with a precision of < ± 0.2 m (2σ) and < ± 26 years uncertainties (95% highest density region). The data show a RSL fall of 0.31 ± 0.18 m between 2.8 and 0.6 thousand years before present (kyr BP), at rates between - 0.1 ± 0.3 and - 0.2 ± 0.7 mm/year. Surface profiles of the fossil coral microatolls suggest fluctuations in the rate of RSL fall: (1) stable between 2.8 and 2.5 kyr BP; (2) rising at ~ 1.8 kyr BP; and (3) stable from 0.8 to 0.6 kyr BP. The microatoll record shows general agreement with published, high-quality RSL data within the Sunda Shelf. Comparison to a suite of glacial isostatic adjustment (GIA) models indicate preference for lower viscosities in the mantle. However, more high quality and precise Late Holocene RSL data are needed to further evaluate the drivers of RSL change in the region and better constrain GIA model parameters.

Local expression of interleukin-2 by B16 melanoma cells results in decreased tumour growth and long-term tumour dormancy.

The tumour microenvironment is complex containing not only neoplastic cells but also a variety of host cells. The heterogeneous infiltrating immune cells include subsets of cells with opposing functions, whose activities are mediated either directly or through the cytokines they produce. Systemic delivery of cytokines such as interleukin-2 ( IL-2) has been used clinically to enhance anti-tumour responses, but these molecules are generally thought to have evolved to act locally in a paracrine fashion. In this study we examined the effect of local production of IL-2 on the growth and the immune response to B16 melanoma cells. We found that the local production of IL-2 enhances the number of interferon-γ-expressing CD8 T and natural killer cells in the tumour, as well as inducing expression of vascular cell adhesion molecule 1 on tumour vessels. These responses were largely absent in interferon-γ knockout mice. The expression of IL-2 in the tumour microenvironment decreases tumour growth despite also enhancing Foxp3(+)  CD4(+) regulatory T cells and anti-inflammatory cytokines such as IL-10. Higher levels of IL-2 in the tumour microenvironment eliminated the progressive growth of the B16 cells in vivo, and this inhibition was dependent on the presence of either T cells or, to a lesser extent, natural killer cells. Surprisingly however, the B16 tumours were not completely eliminated but instead were controlled for an extended period of time, suggesting that a form of tumour dormancy was established.

An evaluation of an expert system for detecting critical events during anesthesia in a human patient simulator: a prospective randomized controlled study.

BACKGROUND: Perioperative monitoring systems produce a large amount of uninterpreted data, use threshold alarms prone to artifacts, and rely on the clinician to continuously visually track changes in physiological data. To address these deficiencies, we developed an expert system that provides real-time clinical decisions for the identification of critical events. We evaluated the efficacy of the expert system for enhancing critical event detection in a simulated environment. We hypothesized that anesthesiologists would identify critical ventilatory events more rapidly and accurately with the expert system. METHODS: We used a high-fidelity human patient simulator to simulate an operating room environment. Participants managed 4 scenarios (anesthetic vapor overdose, tension pneumothorax, anaphylaxis, and endotracheal tube cuff leak) in random order. In 2 of their 4 scenarios, participants were randomly assigned to the expert system, which provided trend-based alerts and potential differential diagnoses. Time to detection and time to treatment were measured. Workload questionnaires and structured debriefings were completed after each scenario, and a usability questionnaire at the conclusion of the session. Data were analyzed using a mixed-effects linear regression model; Fisher exact test was used for workload scores. RESULTS: Twenty anesthesiology trainees and 15 staff anesthesiologists with a combined median (range) of 36 (29-66) years of age and 6 (1-38) years of anesthesia experience participated. For the endotracheal tube cuff leak, the expert system caused mean reductions of 128 (99% confidence interval [CI], 54-202) seconds in time to detection and 140 (99% CI, 79-200) seconds in time to treatment. In the other 3 scenarios, a best-case decrease of 97 seconds (lower 99% CI) in time to diagnosis for anaphylaxis and a worst-case increase of 63 seconds (upper 99% CI) in time to treatment for anesthetic vapor overdose were found. Participants were highly satisfied with the expert system (median score, 2 on a scale of 1-7). Based on participant debriefings, we identified avoidance of task fixation, reassurance to initiate invasive treatment, and confirmation of a suspected diagnosis as 3 safety-critical areas. CONCLUSION: When using the expert system, clinically important and statistically significant decreases in time to detection and time to treatment were observed for the endotracheal tube cuff Leak scenario. The observed differences in the other 3 scenarios were much smaller and not statistically significant. Further evaluation is required to confirm the clinical utility of real-time expert systems for anesthesia.

Monitoring nociception during general anesthesia with cardiorespiratory coherence.

A novel wavelet transform cardiorespiratory coherence (WTCRC) algorithm has been developed to measure the autonomic state. WTCRC may be used as a nociception index, ranging from 0 (no nociception, strong coherence) to 100 (strong nociception, low coherence). The aim of this study is to estimate the sensitivity of the algorithm to nociception (dental dam insertions) and antinociception (bolus doses of anesthetic drugs). WTCRC's sensitivity is compared to mean heart rate (HRmean) and mean non-invasive blood pressure (NIBPmean), which are commonly used clinical signs. Data were collected from 48 children receiving general anesthesia during dental surgery. The times of dental dam insertion and anesthetic bolus events were noted in real-time during surgeries. 42 dental dam insertion and 57 anesthetic bolus events were analyzed. The change in average WTCRC, HRmean, and NIBPmean was calculated between a baseline period before each event and a response period after. A Wilcoxon rank-sum test was used to compare changes. Dental dam insertion changed the WTCRC nociception index by an average of 14 (82 %) [95 % CI from 7.4 to 19], HRmean by 7.3 beats/min (8.1 %) [5.6-9.6], and NIBPmean by 8.3 mmHg (12 %) [4.9-13]. A bolus dose of anesthetics changed the WTCRC by -15 (-50 %) [-21 to -9.3], HRmean by -4.8 beats/min (4.6 %) [-6.6 to -2.9], and NIBPmean by -2.6 mmHg (3.4 %) [-4.7 to -0.50]. A nociception index based on cardiorespiratory coherence is more sensitive to nociception and antinociception than are HRmean or NIBPmean. The WTCRC algorithm shows promise for noninvasively monitoring nociception during general anesthesia.

ERNet: An Efficient and Reliable Human-Object Interaction Detection Network.

Human-Object Interaction (HOI) detection recognizes how persons interact with objects, which is advantageous in autonomous systems such as self-driving vehicles and collaborative robots. However, current HOI detectors are often plagued by model inefficiency and unreliability when making a prediction, which consequently limits its potential for real-world scenarios. In this paper, we address these challenges by proposing ERNet, an end-to-end trainable convolutional-transformer network for HOI detection. The proposed model employs an efficient multi-scale deformable attention to effectively capture vital HOI features. We also put forward a novel detection attention module to adaptively generate semantically rich instance and interaction tokens. These tokens undergo pre-emptive detections to produce initial region and vector proposals that also serve as queries which enhances the feature refinement process in the transformer decoders. Several impactful enhancements are also applied to improve the HOI representation learning. Additionally, we utilize a predictive uncertainty estimation framework in the instance and interaction classification heads to quantify the uncertainty behind each prediction. By doing so, we can accurately and reliably predict HOIs even under challenging scenarios. Experiment results on the HICO-Det, V-COCO, and HOI-A datasets demonstrate that the proposed model achieves state-of-the-art performance in detection accuracy and training efficiency. Codes are publicly available at https://github.com/Monash-CyPhi-AI-Research-Lab/ernet.

Cross-Ancestry Genome-Wide Association Study Defines the Extended CYP2D6 Locus as the Principal Genetic Determinant of Endoxifen Plasma Concentrations.

The therapeutic efficacy of tamoxifen is predominantly mediated by its active metabolites 4-hydroxy-tamoxifen and endoxifen, whose formation is catalyzed by the polymorphic cytochrome P450 2D6 (CYP2D6). Yet, known CYP2D6 polymorphisms only partially determine metabolite concentrations in vivo. We performed the first cross-ancestry genome-wide association study with well-characterized patients of European, Middle-Eastern, and Asian descent (n = 497) to identify genetic factors impacting active and parent metabolite formation. Genome-wide significant variants were functionally evaluated in an independent liver cohort (n = 149) and in silico. Metabolite prediction models were validated in two independent European breast cancer cohorts (n = 287, n = 189). Within a single 1-megabase (Mb) region of chromosome 22q13 encompassing the CYP2D6 gene, 589 variants were significantly associated with tamoxifen metabolite concentrations, particularly endoxifen and metabolic ratio (MR) endoxifen/N-desmethyltamoxifen (minimal P = 5.4E-35 and 2.5E-65, respectively). Previously suggested other loci were not confirmed. Functional analyses revealed 66% of associated, mostly intergenic variants to be significantly correlated with hepatic CYP2D6 activity or expression (ρ = 0.35 to -0.52), and six hotspot regions in the extended 22q13 locus impacting gene regulatory function. Machine learning models based on hotspot variants (n = 12) plus CYP2D6 activity score (AS) increased the explained variability (~ 9%) compared with AS alone, explaining up to 49% (median R2 ) and 72% of the variability in endoxifen and MR endoxifen/N-desmethyltamoxifen, respectively. Our findings suggest that the extended CYP2D6 locus at 22q13 is the principal genetic determinant of endoxifen plasma concentration. Long-distance haplotypes connecting CYP2D6 with adjacent regulatory sites and nongenetic factors may account for the unexplained portion of variability.

Identification by families of pediatric adverse events and near misses overlooked by health care providers.

BACKGROUND: Identifying adverse events and near misses is essential to improving safety in the health care system. Patients are capable of reliably identifying and reporting adverse events. The effect of a patient safety reporting system used by families of pediatric inpatients on reporting of adverse events by health care providers has not previously been investigated. METHODS: Between Nov. 1, 2008, and Nov. 30, 2009, families of children discharged from a single ward of British Columbia's Children's Hospital were asked to respond to a questionnaire about adverse events and near misses during the hospital stay. Rates of reporting by health care providers for this period were compared with rates for the previous year. Family reports for specific incidents were matched with reports by health care providers to determine overlap. RESULTS: A total of 544 familes responded to the questionnaire. The estimated absolute increase in reports by health care providers per 100 admissions was 0.5% (95% confidence interval -1.8% to 2.7%). A total of 321 events were identified in 201 of the 544 family reports. Of these, 153 (48%) were determined to represent legitimate patient safety concerns. Only 8 (2.5%) of the adverse events reported by families were also reported by health care providers. INTERPRETATION: The introduction of a family-based system for reporting adverse events involving pediatric inpatients, administered at the time of discharge, did not change rates of reporting of adverse events and near misses by health care providers. Most reports submitted by families were not duplicated in the reporting system for health care providers, which suggests that families and staff members view safety-related events differently. However, almost half of the family reports represented legitimate patient safety concerns. Families appeared capable of providing valuable information for improving the safety of pediatric inpatients.