HAT: de novo variant calling for highly accurate short-read and long-read sequencing data.

MOTIVATION: de novo variants (DNVs) are variants that are present in offspring but not in their parents. DNVs are both important for examining mutation rates as well as in the identification of disease-related variation. While efforts have been made to call DNVs, calling of DNVs is still challenging from parent-child sequenced trio data. We developed Hare And Tortoise (HAT) as an automated DNV detection workflow for highly accurate short-read and long-read sequencing data. Reliable detection of DNVs is important for human genomics and HAT addresses this need. RESULTS: HAT is a computational workflow that begins with aligned read data (i.e. CRAM or BAM) from a parent-child sequenced trio and outputs DNVs. HAT detects high-quality DNVs from Illumina short-read whole-exome sequencing, Illumina short-read whole-genome sequencing, and highly accurate PacBio HiFi long-read whole-genome sequencing data. The quality of these DNVs is high based on a series of quality metrics including number of DNVs per individual, percent of DNVs at CpG sites, and percent of DNVs phased to the paternal chromosome of origin. AVAILABILITY AND IMPLEMENTATION: https://github.com/TNTurnerLab/HAT.

Advancing Recyclable Thermosets through C═C/C═N Dynamic Covalent Metathesis Chemistry.

Thermoset polymers have become integral to our daily lives due to their exceptional durability, making them feasible for a myriad of applications; however, this ubiquity also raises serious environmental concerns. Covalent adaptable networks (CANs) with dynamic covalent linkages that impart efficient reprocessability and recyclability to thermosets have garnered increasing attention. While various dynamic exchange reactions have been explored in CANs, many rely on the stimuli of active nucleophilic groups and/or catalysts, introducing performance instability and escalating the initial investment. Herein, we propose a new direct and catalyst-free C═C/C═N metathesis reaction between α-cyanocinnamate and aldimine as a novel dynamic covalent motif for constructing recyclable thermosets. This chemistry offers mild reaction conditions (room temperature and catalyst-free), ensuring high yields and simple isolation procedures. By incorporating dynamic C═C/C═N linkages into covalently cross-linked polymer networks, we obtained dynamic thermosets that exhibit both malleability and reconfigurability. The resulting tunable dynamic properties, coupled with the high thermal stability and recyclability of the C═C/C═N linkage-based networks, enrich the toolbox of dynamic covalent chemistry.

de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project.

Detection of de novo variants (DNVs) is critical for studies of disease-related variation and mutation rates. To accelerate DNV calling, we developed a graphics processing units-based workflow. We applied our workflow to whole-genome sequencing data from three parent-child sequenced cohorts including the Simons Simplex Collection (SSC), Simons Foundation Powering Autism Research (SPARK), and the 1000 Genomes Project (1000G) that were sequenced using DNA from blood, saliva, and lymphoblastoid cell lines (LCLs), respectively. The SSC and SPARK DNV callsets were within expectations for number of DNVs, percent at CpG sites, phasing to the paternal chromosome of origin, and average allele balance. However, the 1000G DNV callset was not within expectations and contained excessive DNVs that are likely cell line artifacts. Mutation signature analysis revealed 30% of 1000G DNV signatures matched B-cell lymphoma. Furthermore, we found variants in DNA repair genes and at Clinvar pathogenic or likely-pathogenic sites and significant excess of protein-coding DNVs in IGLL5; a gene known to be involved in B-cell lymphomas. Our study provides a new rapid DNV caller for the field and elucidates important implications of using sequencing data from LCLs for reference building and disease-related projects.

ACES: Analysis of Conservation with an Extensive list of Species.

MOTIVATION: An abundance of new reference genomes is becoming available through large-scale sequencing efforts. While the reference FASTA for each genome is available, there is currently no automated mechanism to query a specific sequence across all new reference genomes. RESULTS: We developed ACES (Analysis of Conservation with an Extensive list of Species) as a computational workflow to query specific sequences of interest (e.g. enhancers, promoters, exons) against reference genomes with an available reference FASTA. This automated workflow generates BLAST hits against each of the reference genomes, a multiple sequence alignment file, a graphical fragment assembly file and a phylogenetic tree file. These data files can then be used by the researcher in several ways to provide key insights into conservation of the query sequence. AVAILABILITY AND IMPLEMENTATION: ACES is available at https://github.com/TNTurnerLab/ACES. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism.

BACKGROUND: Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. RESULTS: We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10-3), and combined dataset (p = 1.1 × 10-4). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10-35, loss-of-function p = 2.26 × 10-13) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10-6, OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. CONCLUSIONS: In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.

The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development.

The MLR COMPASS complex monomethylates H3K4 that serves to epigenetically mark transcriptional enhancers to drive proper gene expression during animal development. Chromatin enrichment analyses of the Drosophila MLR complex reveals dynamic association with promoters and enhancers in embryos with late stage enrichments biased toward both active and poised enhancers. RNAi depletion of the Cmi (also known as Lpt) subunit that contains the chromatin binding PHD finger domains attenuates enhancer functions, but unexpectedly results in inappropriate enhancer activation during stages when hormone responsive enhancers are poised, revealing critical epigenetic roles involved in both the activation and repression of enhancers depending on developmental context. Cmi is necessary for robust H3K4 monomethylation and H3K27 acetylation that mark active enhancers, but not for the chromatin binding of Trr, the MLR methyltransferase. Our data reveal two likely major regulatory modes of MLR function, contributions to enhancer commissioning in early embryogenesis and bookmarking enhancers to enable rapid transcriptional re-activation at subsequent developmental stages.

Clinical Outcomes of Complications Following Self-Expandable Metallic Stent Insertion for Benign Tracheobronchial Stenosis.

Background and Objectives: The use of metallic stents in benign TBS is controversial. Here, we report the clinical outcomes of patients who developed complications due to self-expandable metallic stent (SEMS) insertion for benign TBS. Materials and Methods: Our institution, which is the largest and most active referral hospital for airway stenosis in South Korea, only uses silicone stents. We conducted a retrospective review of 20 patients referred after the insertion of SEMS for benign TBS from 2006 to 2015. Results: All 20 patients underwent rigid bronchoscopy for SEMS removal due to airway obstruction from granulation tissue overgrowth. All but one (95%) experienced successful removal of the SEMS. During a median follow-up period of 40 months, a median of seven rigid bronchoscopies per patient was needed to maintain airway patency. Three (15%) patients suffered acute complications during SEMS removal (bleeding (10%) and fistula (5%)). All patients suffered chronic complications (granulation tissue (80%), stent migration (58%), mucostasis (55%), and restenosis (43%)). Eventually, 15 patients (75%) needed airway prostheses (silicone stent (75%) and tracheostomy (25%)). Conclusion: Our findings indicate that SEMS should be avoided until positive results are consistently reported by high-quality studies in patients with benign TBS.

Cost-effectiveness of a transitional home-based palliative care program for patients with end-stage heart failure.

BACKGROUND: Studies have shown positive clinical outcomes of specialist palliative care for end-stage heart failure patients, but cost-effectiveness evaluation is lacking. AIM: To examine the cost-effectiveness of a transitional home-based palliative care program for patients with end-stage heart failure patients as compared to the customary palliative care service. DESIGN: A cost-effectiveness analysis was conducted alongside a randomized controlled trial (Trial number: NCT02086305). The costs included pre-program training, intervention, and hospital use. Quality of life was measured using SF-6D. SETTING/PARTICIPANTS: The study took place in three hospitals in Hong Kong. The inclusion criteria were meeting clinical indicators for end-stage heart failure patients including clinician-judged last year of life, discharged to home within the service area, and palliative care referral accepted. A total of 84 subjects (study = 43, control = 41) were recruited. RESULTS: When the study group was compared to the control group, the net incremental quality-adjusted life years gain was 0.0012 (28 days)/0.0077 (84 days) and the net incremental costs per case was -HK$7935 (28 days)/-HK$26,084 (84 days). The probability of being cost-effective was 85% (28 days)/100% (84 days) based on the cost-effectiveness thresholds recommended both by National Institute for Health and Clinical Excellence (£20,000/quality-adjusted life years) and World Health Organization (Hong Kong gross domestic product/capita in 2015, HK$328117). CONCLUSION: Results suggest that a transitional home-based palliative care program is more cost-effective than customary palliative care service. Limitations of the study include small sample size, study confined to one city, clinic consultation costs, and societal costs including patient costs and unpaid care-giving costs were not included.

Enantioselective Chemical Syntheses of the Furanosteroids (-)-Viridin and (-)-Viridiol.

Herein we describe concise enantioselective chemical syntheses of (-)-viridin and (-)-viridiol. Our convergent approach couples two achiral fragments of similar complexity and employs an enantioselective intramolecular Heck reaction to set the absolute stereochemical configuration of an all-carbon quaternary stereocenter. To complete the syntheses of these base- and nucleophile-sensitive natural products, we conduct carefully orchestrated site- and diastereoselective oxidations and other transformations. Our work is the first to generate these targets as single enantiomers.

Basic critical care echocardiography by pulmonary fellows: learning trajectory and prognostic impact using a minimally resourced training model*.

OBJECTIVES: The spread of basic critical care echocardiography may be limited by training resources. Another barrier is the lack of information about the learning trajectory and prognostic impact of individual basic critical care echocardiography domains like acute cor pulmonale determination and left ventricular function estimation. We thus developed a minimally resourced training model and studied the latter outcomes. DESIGN: Prospective observational study. SETTING: Twenty-bed medical ICU. SUBJECTS: Echocardiography-naive trainees enrolled in the first year of our Pulmonary Medicine Fellowship Program from September 2012 to September 2013. INTERVENTIONS: We described the learning trajectory in six basic critical care echocardiography domains (adequate views, pericardial effusion, acute cor pulmonale, left ventricular ejection fraction, mitral regurgitation, and inferior vena cava variability) and correlated abnormalities in selected basic critical care echocardiography domains with clinical outcomes (mortality and length of stay). MEASUREMENTS AND MAIN RESULTS: Three-hundred forty-three basic critical care echocardiography scans were done for 318 patients by seven fellows (median of 40 scans per fellow; range, 34-105). Only one-third patients had normal basic critical care echocardiography studies. Accuracy in various basic critical care echocardiography domains was high (> 90%), especially beyond the first 30 examinations. Acute cor pulmonale was associated with ICU mortality when adjusted for Acute Physiology and Chronic Health Evaluation II score and presence of sepsis, whereas mitral regurgitation was associated with longer hospitalization only on univariate analysis. CONCLUSIONS: Basic critical care echocardiography training using minimal resources is feasible. New trainees can achieve reasonable competency in most basic critical care echocardiography domains after performing about 30 examinations within the first year. The relatively high prevalence of abnormalities and the significant association of acute cor pulmonale with ICU mortality support the need for basic critical care echocardiography training.

Proteome-Wide Assessment of Clustering of Missense Variants in Neurodevelopmental Disorders Versus Cancer.

Missense de novo variants (DNVs) and missense somatic variants contribute to neurodevelopmental disorders (NDDs) and cancer, respectively. Proteins with statistical enrichment based on analyses of these variants exhibit convergence in the differing NDD and cancer phenotypes. Herein, the question of why some of the same proteins are identified in both phenotypes is examined through investigation of clustering of missense variation at the protein level. Our hypothesis is that missense variation is present in different protein locations in the two phenotypes leading to the distinct phenotypic outcomes. We tested this hypothesis in 1D protein space using our software CLUMP. Furthermore, we newly developed 3D-CLUMP that uses 3D protein structures to spatially test clustering of missense variation for proteome-wide significance. We examined missense DNVs in 39,883 parent-child sequenced trios with NDDs and missense somatic variants from 10,543 sequenced tumors covering five TCGA cancer types and two COSMIC pan-cancer aggregates of tissue types. There were 57 proteins with proteome-wide significant missense variation clustering in NDDs when compared to cancers and 79 proteins with proteome-wide significant missense clustering in cancers compared to NDDs. While our main objective was to identify differences in patterns of missense variation, we also identified a novel NDD protein BLTP2. Overall, our study is innovative, provides new insights into differential missense variation in NDDs and cancer at the protein-level, and contributes necessary information toward building a framework for thinking about prognostic and therapeutic aspects of these proteins.

Are changes in pain intensity related to changes in balance control in individuals with chronic non-specific low back pain? A systematic review and meta-analysis.

PURPOSE: The aim of this study is to summarize the evidence regarding whether pain reduction in individuals with chronic non-specific low back pain (CNSLBP) following conservative interventions is related to corresponding improvements in balance control. METHODS: Randomized controlled trials were identified from 5 databases (MEDLINE, Cochrane Library, Embase, Web of Science, and PsycINFO). Two reviewers independently screened and identified relevant studies that investigated the effects of nonsurgical or nonpharmacological CNSLBP treatments on both pain intensity and balance control. Meta-regression analyses were performed to establish the associations between post-treatment changes in these 2 variables. RESULTS: 31 studies involving 1280 participants with CNSLBP were included. Moderate-quality evidence suggested that pain reduction was associated with and explained 34%-45% of decreases in body sway, as measured by center-of-pressure (CoP) area and CoP velocity with eyes open. However, no significant association was observed between pain reduction and CoP area or velocity in anteroposterior/mediolateral directions. Similarly, there was no significant association between pain reduction and CoP distance or radius. Low-quality evidence indicated that pain relief explained a 15% improvement in one-leg stance with eyes open but not in the eyes-closed condition. Additionally, very low-quality evidence suggested that pain relief explained a 44% decrease in the static anteroposterior stability index with eyes closed but not in the eyes-open, mediolateral, or overall conditions. Furthermore, low-quality evidence indicated that reduced pain was associated with and accounted for 25%-43% of the improved composite and posteromedial scores of the star-excursion balance test, rather than the anterior and posterolateral scores. CONCLUSION: Depending on the type of balance assessment, pain relief following conservative interventions may slightly to moderately enhance balance control in individuals with CNSLBP. Clinicians should pay close attention to the balance control in patients with CNSLBP, particularly among older adults.

Internal migration of nurses in the United States: migratory prompts and difference in job satisfaction between migrants and non-migrants.

In the United States, nurses are highly mobile due to a nursing shortage and the transferability of their skills. Despite the importance of internal migration (inter-state movement) of nurses in the distribution of the supply nurses, little is known about such migration. Researchers used data from the 2004 and 2008 National Sample Survey of Registered Nurses to examine the factors associated with nurses' internal migration as well as the difference in job satisfaction for migrant and non-migrant nurses. Factors associated with a higher likelihood of internal migration were: a change in employer, higher earnings, not foreign-educated, less nursing experience, a younger age, being male, being single, having no children, the Nursing Licensure Compact, and not being employed in the state where the first RN license was obtained. Migrant nurses had lower job satisfaction than non-migrant nurses; higher job satisfaction is noted with higher earnings levels. The development of policies such as relocation and social support to help migrant nurses cope and adjust to a new working environment are proposed.

HAT: de novo variant calling for highly accurate short-read and long-read sequencing data.

Motivation: de novo variant (DNV) calling is challenging from parent-child sequenced trio data. We developed Hare And Tortoise (HAT) to work as an automated workflow to detect DNVs in highly accurate short-read and long-read sequencing data. Reliable detection of DNVs is important for human genetics studies (e.g., autism, epilepsy). Results: HAT is a workflow to detect DNVs from short-read and long read sequencing data. This workflow begins with aligned read data (i.e., CRAM or BAM) from a parent-child sequenced trio and outputs DNVs. HAT detects high-quality DNVs from short-read whole-exome sequencing, short-read whole-genome sequencing, and highly accurate long-read sequencing data.

Diagnostic Yield and Safety of CP-EBUS-TBNA and RP-EBUS-TBLB under Moderate Sedation: A Single-Center Retrospective Audit.

Convex probe endobronchial ultrasound transbronchial needle aspirations (CP-EBUS-TBNAs) and radial probe endobronchial ultrasound transbronchial lung biopsies (RP-EBUS-TBLBs) can be performed under moderate sedation or general anesthesia. Moderate sedation is more convenient, however patient discomfort may result in inadequate tissue sampling. General anesthesia ensures better patient cooperation but requires more logistics and also carries sedation risks. We aim to describe the diagnostic yield and safety of CP-EBUS-TBNAs and RP-EBUS-TBLBs when performed under moderate sedation at our center. All patients who underwent CP-EBUS-TBNA and/or RP-EBUS-TBLB under moderate sedation, between January 2015 and May 2017, were reviewed. Primary outcomes were defined in regard to the diagnostic yield and safety profile. A total of 336 CP-EBUS-TBNAs and 190 RP-EBUS-TBLBs were performed between January 2015 and May 2017. The mean sedation doses used were 50 mcg of intravenous fentanyl and 2.5 mg of intravenous midazolam. The diagnostic yield of the CP-EBUS-TBNAs and RP-EBUS-TBLBs were 62.5% and 71.6%, respectively. Complication rates were low with: transient bleeding 11.9%, transient hypoxia 0.5%, and pneumothorax 0.1%. None required escalation of care, post procedure. Performing CP-EBUS-TBNAs and RP-EBUS-TBLBs under moderate sedation is safe and provides good diagnostic yield. These procedures should, therefore, be considered as first-line sampling techniques.

From karyotypes to precision genomics in 9p deletion and duplication syndromes.

While 9p deletion and duplication syndromes have been studied for several years, small sample sizes and minimal high-resolution data have limited a comprehensive delineation of genotypic and phenotypic characteristics. In this study, we examined genetic data from 719 individuals in the worldwide 9p Network Cohort: a cohort seven to nine times larger than any previous study of 9p. Most breakpoints occur in bands 9p22 and 9p24, accounting for 35% and 38% of all breakpoints, respectively. Bands 9p11 and 9p12 have the fewest breakpoints, with each accounting for 0.6% of all breakpoints. The most common phenotype in 9p deletion and duplication syndromes is developmental delay, and we identified eight known neurodevelopmental disorder genes in 9p22 and 9p24. Since it has been previously reported that some individuals have a secondary structural variant related to the 9p variant, we examined our cohort for these variants and found 97 events. The top secondary variant involved 9q in 14 individuals (1.9%), including ring chromosomes and inversions. We identified a gender bias with significant enrichment for females (p = 0.0006) that may arise from a sex reversal in some individuals with 9p deletions. Genes on 9p were characterized regarding function, constraint metrics, and protein-protein interactions, resulting in a prioritized set of genes for further study. Finally, we achieved precision genomics in one child with a complex 9p structural variation using modern genomic technologies, demonstrating that long-read sequencing will be integral for some cases. Our study is the largest ever on 9p-related syndromes and provides key insights into genetic factors involved in these syndromes.

Clostridium difficile toxin-induced inflammation and intestinal injury are mediated by the inflammasome.

BACKGROUND & AIMS: Clostridium difficile-associated disease (CDAD) is the leading cause of nosocomial diarrhea in the United States. C difficile toxins TcdA and TcdB breach the intestinal barrier and trigger mucosal inflammation and intestinal damage. The inflammasome is an intracellular danger sensor of the innate immune system. In the present study, we hypothesize that TcdA and TcdB trigger inflammasome-dependent interleukin (IL)-1beta production, which contributes to the pathogenesis of CDAD. METHODS: Macrophages exposed to TcdA and TcdB were assessed for IL-1beta production, an indication of inflammasome activation. Macrophages deficient in components of the inflammasome were also assessed. Truncated/mutated forms of TcdB were assessed for their ability to activate the inflammasome. The role of inflammasome signaling in vivo was assessed in ASC-deficient and IL-1 receptor antagonist-treated mice. RESULTS: TcdA and TcdB triggered inflammasome activation and IL-1beta secretion in macrophages and human mucosal biopsy specimens. Deletion of Nlrp3 decreased, whereas deletion of ASC completely abolished, toxin-induced IL-1beta release. TcdB-induced IL-1beta release required recognition of the full-length toxin but not its enzymatic function. In vivo, deletion of ASC significantly reduced toxin-induced inflammation and damage, an effect that was mimicked by pretreatment with the IL-1 receptor antagonist anakinra. CONCLUSIONS: TcdA and TcdB trigger IL-1beta release by activating an ASC-containing inflammasome, a response that contributes to toxin-induced inflammation and damage in vivo. Pretreating mice with the IL-1 receptor antagonist anakinra afforded the same level of protection that was observed in ASC-/- mice. These data suggest that targeting inflammasome or IL-1beta signaling may represent new therapeutic targets in the treatment of CDAD.

Hypoxia-inducible factor signaling provides protection in Clostridium difficile-induced intestinal injury.

BACKGROUND & AIMS: Clostridium difficile is the leading cause of nosocomial infectious diarrhea. Antibiotic resistance and increased virulence of strains have increased the number of C difficile-related deaths worldwide. The innate host response mechanisms to C difficile are not resolved; we propose that hypoxia-inducible factor (HIF-1) has an innate, protective role in C difficile colitis. We studied the impact of C difficile toxins on the regulation of HIF-1 and evaluated the role of HIF-1alpha in C difficile-mediated injury/inflammation. METHODS: We assessed HIF-1alpha mRNA and protein levels and DNA binding in human mucosal biopsy samples and Caco-2 cells following exposure to C difficile toxins. We used the mouse ileal loop model of C difficile toxin-induced intestinal injury. Mice with targeted deletion of HIF-1alpha in the intestinal epithelium were used to assess the effects of HIF-1alpha signaling in response to C difficile toxin. RESULTS: Mucosal biopsy specimens and Caco-2 cells exposed to C difficile toxin had a significant increase in HIF-1alpha transcription and protein levels. Toxin-induced DNA binding was also observed in Caco-2 cells. Toxin-induced HIF-1alpha accumulation was attenuated by nitric oxide synthase inhibitors. In vivo deletion of intestinal epithelial HIF-1alpha resulted in more severe, toxin-induced intestinal injury and inflammation. In contrast, stabilization of HIF-1alpha with dimethyloxallyl glycine attenuated toxin-induced injury and inflammation. This was associated with induction of HIF-1-regulated protective factors (such as vascular endothelial growth factor-alpha, CD73, and intestinal trefoil factor) and down-regulation of proinflammatory molecules such as tumor necrosis factor and Cxcl1. CONCLUSIONS: HIF-1alpha protects the intestinal mucosa from C difficile toxins. The innate protective actions of HIF-1alpha in response to C difficile toxins be developed as therapeutics for C difficile-associated disease.

Transitioning to Combined EBUS EUS-B FNA for Experienced EBUS Bronchoscopist.

Endobronchial ultrasound (EBUS) combined with trans-esophageal endoscopic ultrasound bronchoscope guided fine need aspirate (EUS-B FNA) of mediastinal lymph nodes is an established procedure for diagnosis. The main barrier to a combined EBUS EUS-B FNA approach is availability of trained and accredited pulmonologist who can perform procedure safely and confidently. To address this gap, we undertook a training program for experienced EBUS bronchoscopists to train, learn, and incorporate combined EBUS EUS-B FNA into their procedural practice. Thirty-two patients were selected based on CT and or PET findings. Four experienced bronchoscopists participated by reading through learning material, observing 5 cases before performing EUS-B FNA under direct supervision. Forty-one lymph nodes and 6 non-nodal lesions were sampled. EUSAT assessment was performed by supervisor. Learning curves were derived from assessment scores. We observed that learning curve tends to plateau when participant can perform 3 or more consecutive cases with EUSAT score above 50. There were no complications. Our experience suggests that there is relative ease in transition to combined EBUS EUS-B TBNA procedures for mediastinal lymphadenopathy and lung cancer diagnosis and staging for experienced bronchoscopist using a program which incorporates direct supervision, EUSAT assessment, and extension of EUS B FNA training into daily real-world practice.

Healthcare professionals' perceptions of existential distress in patients with advanced cancer.

AIM: This paper is a report of an exploration of the phenomenon of existential distress in patients with advanced cancer from the perspectives of healthcare professionals. BACKGROUND: Existential distress is an important concern in patients with advanced cancer; it affects their well-being and needs to be addressed in the provision of holistic care. METHOD: Focus groups were conducted from November 2008 to February 2009 with physicians, nurses, social workers, occupational therapists, physiotherapists, and chaplains working in a palliative care unit that served patients with advanced cancer in Hong Kong. Data collection and analysis were guided by the grounded theory approach. All categories were saturated when five focus groups had been held with a total number of 23 participants. FINDINGS: We found three causal conditions of existential distress: anticipation of a negative future, failure to engage in meaningful activities and relationships, and having regrets. Three basic (caring, relating and knowing) and six specific (positive feedback, religious support, new experiences, task setting, exploring alternatives and relationship reconciliation) intervening strategies were identified. Whether the intervening strategies would be effective would depend on patients' openness and readiness; healthcare professionals' self-awareness, hopefulness, and interest in knowing the patients; and a trusting relationship between patients and healthcare professionals. A sense of peace in patients was considered a consequence of successful interventions. CONCLUSION: This paper acknowledges the lack of an accepted conceptual framework of existential distress in patients with advanced cancer. It is based on healthcare professionals' views, and further studies from the perspectives of patients and their families are needed.