Technical and analytical approach to biventricular pressure-volume loops in swine including a completely endovascular, percutaneous closed-chest large animal model.

Pressure-volume (PV) loop analysis is a sophisticated invasive approach to quantifying load-dependent and independent measures of cardiac function. Biventricular (BV) PV loops allow left and right ventricular function to be quantified simultaneously and independently, which is important for conditions and certain physiologic states, such as ventricular decoupling or acute physiologic changes. BV PV loops can be performed in an entirely endovascular, percutaneous, and closed-chest setting. This technique is helpful in a survival animal model, as a percutaneous monitoring system during endovascular device experiments, or in cases where chest wall compliance is being tested or may be a confounder. In this article, we describe the end-to-end implementation of a completely endovascular, totally percutaneous, and closed-chest large animal model to obtain contemporaneous BV PV loops in 40 to 70 kg swine. We describe the associated surgical and technical challenges and our solutions to obtaining endovascular BV PV loops, closed-chest cardiac output, and stroke volume (including validation of the correction factor necessary for thermodilution), as well as how to perform endovascular inferior vena cava occlusion in this swine model. We also include techniques for data acquisition and analysis that are required for this method.

Docetaxel-Based Neoadjuvant Chemotherapy Followed by En Bloc Resection for Esophageal Adenocarcinoma: A 15-Year Retrospective Analysis from a Regional Upper Gastrointestinal Cancer Network.

BACKROUND: Real-world, long-term survival outcomes of neoadjuvant, docetaxel-based therapy for esophageal and junctional adenocarcinoma are lacking. This study describes the long-term survival outcomes of patients with esophageal and junctional adenocarcinoma treated with neoadjuvant docetaxel-based chemotherapy and en bloc transthoracic esophagectomy. METHODS: A retrospective cohort analysis of a prospectively maintained database from a regional upper gastrointestinal cancer network in Quebec, Canada, was performed. From January 2007 to December 2021, all patients with locally advanced (cT3 and/or N1) esophageal/Siewert I/II adenocarcinoma treated with neoadjuvant DCFx3 (Docetaxel/Cisplatin/5FU) or FLOTx4 (5FU/Leucovorin/Oxaliplatin/Docetaxel) and transthoracic en bloc esophagectomy were identified. Postoperative, pathological, and survival outcomes were compared. RESULTS: Overall, 236 of 420 patients met the inclusion criteria. Tumor location was esophageal/Siewert I/Siewert II (118/33/85), most were cT3-4 (93.6%) and cN+ (61.0%). DCF and FLOT were used in 127 of 236 (53.8%) and 109 of 236 (46.2%). All neoadjuvant cycles were completed in 87.3% with no difference between the regimens. Operative procedures included Ivor Lewis (81.8%), left thoraco-abdominal esophagectomy (10.6%) and McKeown (7.6%) with an R0 resection in 95.3% and pathological complete response in 9.7% (DCF 12.6%/FLOT 6.4%, p = 0.111). The median lymph node yield was 32 (range 4-79), and 60.6% were ypN+. Median follow-up was longer for the DCF group (74.8 months 95% confidence interval [CI] 4-173 vs. 37.8 months 95% CI 2-119, p <0.001. Overall survival was similar between the groups (FLOT 97.3 months, 78.6-115.8 vs. DCF 92.9, 9.2-106.5, p = 0.420). CONCLUSIONS: Neoadjuvant DCF and FLOT followed by transthoracic en bloc resection are both highly effective regimens for locally advanced esophageal adenocarcinoma with equivalent survival outcomes despite high disease load.

Symptom Assessment Following Surgery for Lung Cancer: A Canadian Population-based Retrospective Cohort Study.

OBJECTIVE: To conduct a population-level analysis of temporal trends and risk factors for high symptom burden in patients receiving surgery for non-small cell lung cancer (NSCLC). BACKGROUND: A population-level overview of symptoms after curative intent surgery is necessary to inform decision making and supportive care for patients with lung cancer. METHODS: Retrospective cohort study of patients receiving surgery for stages I to III NSCLC between January 2007 and September 2018. Prospectively collection Edmonton Symptom Assessment System (ESAS) scores, linked to provincial administrative data, were used to describe the prevalence, trajectory, and predictors of moderate-to-severe symptoms in the year following surgery. RESULTS: A total of 5350 patients, with 28,490 unique ESAS assessments, were included in the analysis. Moderate-to-severe tiredness (68%), poor wellbeing (63%), and shortness of breath (60%) were the most common symptoms reported. The rise and fall in the proportion of patients experiencing moderate-to-severe symptoms after surgery coincided with the median time to first (58 days, interquartile range: 47-72) and last cycle of chemotherapy (140 days, interquartile range: 118-168), respectively. There was eventual stabilization, albeit above the preoperative baseline, within 6 to 7 months after surgery. Female sex (relative risk [RR] 1.09- 1.26), lower income (RR 1.08-1.23), stage III disease (RR 1.15-1.43), adjuvant therapy (RR 1.09-1.42), chemotherapy within 2 weeks of an ESAS assessment (RR 1.14-1.73), and pneumonectomy (RR 1.05-1.15) were associated with moderate-to-severe symptoms following surgery. CONCLUSIONS: Knowledge of population-level prevalence, trajectory, and predictors of moderate-to-severe symptoms after surgery for NSCLC can be used to facilitate shared decision making and improve symptom management throughout the course of illness.

Long-term Functional Outcomes Among Older Adults Undergoing Video-assisted Versus Open Surgery for Lung Cancer: A Population-based Cohort Study.

OBJECTIVE: To examine the long-term healthcare dependency outcomes of older adults undergoing VATS compared to open lung cancer resection. SUMMARY OF BACKGROUND DATA: Although the benefits of VATS for lung cancer resection have been reported, there is a knowledge gap related to long-term functional outcomes central to decision-making for older adults. METHODS: We conducted a population-based retrospective comparative cohort study of patients ≥70 years old undergoing lung cancer resection between 2010 and 2017 using linked administrative health databases. VATS was compared to open surgery for lung cancer resection. Outcomes were receipt of homecare and high time-at-home, defined as <14 institution-days within 1 year, in 5 years after surgery. We used time-to-event analyses. Homecare was analyzed as recurrent dichotomous outcome with Andersen-Gill multivariable models, and high time-at-home with Cox multivariable models. RESULTS: Of 4974 patients, 2951 had VATS (59.3%). In the first three months postoperatively, homecare use ranged from 17.5% to 34.4% for VATS and 23.0% to 36.6% for open surgery. VATS was independently associated with lower need for postoperative homecare over 5 years (hazard ratio 0.82, 95% confidence interval 0.74-0.92). 1- and 5-year probability of high "time-at-home" were superior for VATS (74.4% vs 66.7% and 55.6% vs 45.4%, p < 0.001). VATS was independently associated with higher probability of high "time-at-home" (hazard ratio 0.81, 95% confidence interval 0.74-0.89) compared to open surgery. CONCLUSIONS: Compared to open surgery, VATS was associated with lower homecare needs and higher probability of high "time-at-home," indicating reduced long-term functional dependence. Those important patient-centered endpoints reflect the overall long-term treatment burden on mortality and morbidity that can inform surgical decision-making.

Long-term Dependency in Older Adults After Surgery or Stereotactic Body Radiation Therapy for Stage I Non-Small Cell Lung Cancer.

OBJECTIVE: To examine long-term healthcare dependency outcomes of stereotactic body radiation therapy (SBRT) to surgery for older adults with stage I non-small cell lung cancer (NSCLC). BACKGROUND: SBRT is an emerging alternative to surgery in patients with early-stage lung cancer. There remains a paucity of prospective studies comparing these modalities, especially with respect to long-term dependency outcomes in older adults with lung cancer. METHODS: Adults 70 years old and above with stage I NSCLC treated with surgery or SBRT from January 2010 to December 2017 were analyzed using 1:1 propensity score matching. Homecare use, days at home, and time spent alive and at home were compared. E-value methods assessed residual confounding. RESULTS: A total of 1129 and 2570 patients underwent SBRT and surgery, respectively. In all, 1016 per group were matched. SBRT was associated with a higher overall risk of homecare utilization [hazard ratio (HR)=1.75, 95% confidence interval (CI): 1.37-2.23] than surgery up to 5 years following treatment. While the hazards of death or nursing home admission were lower in the first 3 months after SBRT (HR=0.55, 95% CI: 0.36-0.85), they became consistently higher beyond this period and remained high up to 5 years compared with surgery (HR=2.13; 95% CI: 1.85-2.45). The above findings persisted in stratified analyses for frail patients and those with no pretreatment homecare. E-values indicated it was unlikely that the observed estimates could be explained by unmeasured confounders. CONCLUSIONS: Surgery offers robust long-term dependency outcomes compared with SBRT. These are important patient-centered endpoints which may be used for counseling and shared decision-making in older adults with stage I NSCLC.

Evidence reversals in primary care research: a study of randomized controlled trials.

BACKGROUND: Evidence-Based Medicine is built on the premise that clinicians can be more confident when their decisions are grounded in high-quality evidence. Furthermore, evidence from studies involving patient-oriented outcomes is preferred when making decisions about tests or treatments. Ideally, the findings of relevant and valid trials should be stable over time, that is, unlikely to be reversed in subsequent research. OBJECTIVE: To evaluate the stability of evidence from trials relevant to primary healthcare and to identify study characteristics associated with their reversal. METHODS: We studied synopses of randomized controlled trials (RCTs) published from 2002 to 2005 as "Daily POEMs" (Patient Oriented Evidence that Matters). The initial evidence (E1) from these POEMs (2002-2005) was compared with the updated evidence (E2) on that same topic in a summary resource (DynaMed 2019). Two physician-raters independently categorized each POEM-RCT as (i) reversed when E1 ≠ E2, or as (ii) not reversed, when E1 = E2. For all "Evidence Reversals" (E1 ≠ E2), we assessed the direction of change in the evidence. RESULTS: We evaluated 408 POEMs on RCTs. Of those, 35 (9%; 95% confidence interval [6-12]) were identified as reversed, 359 (88%) were identified as not reversed, and 14 (3%) were indeterminate. On average, this represents about 2 evidence reversals per annum for POEMs about RCTs. CONCLUSIONS: Over 12-17 years, 9% of RCTs summarized as POEMs are reversed. Information alerting services that apply strict criteria for relevance and validity of clinical information are likely to identify RCTs whose findings are stable over time.

We studied the extent to which evidence from randomized controlled trials (RCTs) relevant to primary care is contradicted in subsequent research. When it was, we identified this event as an evidence reversal. In addition, we sought to identify characteristics of RCTs associated with their reversal. From 408 RCTs published during the period 2002­2005, study characteristics such as sample size were identified and extracted. Subsequently, we compared the evidence reported in each of these RCTs with the evidence on that same topic in an online summary resource in 2019. This allowed us to classify each RCT in one of the following 3 categories: evidence confirmed, reversed, or uncertain if this evidence is confirmed or reversed. Over 12­17 years of follow-up time, the findings of about 9 in 10 RCTs summarized as POEMs are stable. We found no statistically significant associations between trial characteristics and their subsequent reversal. This low rate of evidence reversal is good news for the RCTs that are used to inform decision-making.

Does spaced education improve clinical knowledge among Family Medicine residents? A cluster randomized controlled trial.

Spaced education is a learning strategy to improve knowledge acquisition and retention. To date, no robust evidence exists to support the utility of spaced education in the Family Medicine residency. We aimed to test whether alerts to encourage spaced education can improve clinical knowledge as measured by scores on the Canadian Family Medicine certification examination. METHOD: We conducted a cluster randomized controlled trial to empirically and pragmatically test spaced education using two versions of the Family Medicine Study Guide mobile app. 12 residency training programs in Canada agreed to participate. At six intervention sites, we consented 335 of the 654 (51%) eligible residents. Residents in the intervention group were sent alerts through the app to encourage the answering of questions linked to clinical cases. At six control sites, 299 of 586 (51%) residents consented. Residents in the control group received the same app but with no alerts. Incidence rates of case completion between trial arms were compared using repeated measures analysis. We linked residents in both trial arms to their knowledge scores on the certification examination of the College of Family Physicians of Canada. RESULTS: Over 67 weeks, there was no statistically significant difference in the completion of clinical cases by participants. The difference in mean exam scores and the associated confidence interval did not exceed the pre-defined limit of 4 percentage points. CONCLUSION: Further research is recommended before deploying spaced educational interventions in the Family Medicine residency to improve knowledge.

Do Weekly Alerts From a Mobile Application Influence Reading During Residency?

BACKGROUND: The benefits of "spaced education" have been documented for residents in highly focused specialties. We found no published studies of spaced education in family medicine. In this study, we report on the feasibility of delivering weekly alerts from a mobile application (app) developed for exam preparation, to increase the reading of clinical information in the family medicine residency. DESIGN: This is a 2-phase mixed methods study. Phase one is a quasi-experimental study of resident reading of information related to priority topics in family medicine. Reading was documented by page views in a noncommercial mobile app. PARTICIPANTS: All incoming first-year residents at two university training programs in Canada. The intervention group received one alert per week to priority topics on the app, beginning in their second month of residency. The control group was given access to the same app, but received no alerts. RESULTS: In this paper, we report the phase one preliminary findings. In the intervention group, 81 of 96 first year residents consented. At the control site, 79 of 85 residents consented. After 100 days, intervention group residents had viewed more pages of clinical information across all 99 priority topics (1,546 versus 900) and per topic (15.7 versus 9.1 pages, P < 0.0003). On average, each increase of one visit to the app following a weekly alert was associated with an increase of 3.2 visits to pages of clinical information in the app. CONCLUSION: A weekly alert delivered via mobile app shows promise with respect to reading in the family medicine residency.

Trauma care and referral patterns in Rwanda: implications for trauma system development.

BACKGROUND: Trauma remains a leading cause of death worldwide. The development of trauma systems in low-resource settings may be of benefit. The objective of this study was to describe operative procedures performed for trauma at a tertiary care facility in Kigali, Rwanda, and to evaluate geographical variations and referral patterns of trauma care. METHODS: We retrospectively reviewed all prospectively collected operative cases performed at the largest referral hospital in Rwanda, the Centre Hospitalier Universitaire de Kigali (CHUK), between June 1 and Dec. 1, 2011, for injury-related diagnoses. We used the Pearson χ² and Fisher exact tests to compare cases arising from within Kigali to those transferred from other provinces. Geospatial analyses were also performed to further elucidate transfer patterns. RESULTS: Over the 6-month study period, 2758 surgical interventions were performed at the CHUK. Of these, 653 (23.7%) were for trauma. Most patients resided outside of Kigali city, with 337 (58.0%) patients transferred from other provinces and 244 (42.0%) from within Kigali. Most trauma procedures were orthopedic (489 [84.2%]), although general surgery procedures represented a higher proportion of trauma surgeries in patients from other provinces than in patients from within Kigali (28 of 337 [8.3%] v. 10 of 244 [4.1%]). CONCLUSION: To our knowledge, this is the first study to highlight geographical variations in access to trauma care in a low-income country and the first description of trauma procedures at a referral centre in Rwanda. Future efforts should focus on maturing prehospital and interfacility transport systems, strengthening district hospitals and further supporting referral institutions.

CONTEXTE: Les traumatismes demeurent l'une des principales causes de décès dans le monde. La mise au point de systèmes de traumatologie dans des milieux défavorisés pourrait toutefois contribuer à améliorer la situation. Notre étude avait pour objectif de décrire les interventions chirurgicales pratiquées sur les victimes de traumatismes dans un établissement de soins tertiaires de Kigali, au Rwanda, et d'évaluer les variations géographiques et les habitudes d'orientation des patients dans le domaine de la traumatologie. MÉTHODES: Nous avons évalué rétroactivement les données recueillies de façon prospective sur l'ensemble des interventions réalisées au plus grand centre hospitalier régional du Rwanda, le Centre hospitalier universitaire de Kigali (CHUK), du 1er juin au 1er décembre 2011 pour les diagnostics liés à des blessures. Nous avons eu recours au test χ² de Pearson et au test exact de Fisher pour comparer les cas issus de la province de Kigali à ceux provenant d'autres provinces. Nous avons en outre effectué des analyses géospatiales afin de mieux comprendre les habitudes d'orientation des patients. RÉSULTATS: Au cours des 6 mois de l'étude, 2758 interventions chirurgicales ont été pratiquées au CHUK, dont 653 (23,7 %) pour des traumatismes. La majorité des patients résidaient à l'extérieur de la capitale : 337 (58,0 %) d'entre eux avaient été transférés d'autres provinces, et 244 (42,0 %), d'ailleurs dans la province. Si la plupart des interventions chirurgicales étaient orthopédiques (489, soit 84,2 %), les patients d'autres provinces ont plus souvent subi des interventions générales que leurs compatriotes de la province de Kigali (28 sur 337, soit 8,3 %, par rapport à 10 sur 244, soit 4,1 %). CONCLUSION: À notre connaissance, il s'agit de la première étude mettant en lumière les variations géographiques de l'accès aux soins en traumatologie dans un pays à faible revenu et de la première description des interventions chirurgicales pratiquées sur des victimes de traumatismes dans un centre régional du Rwanda. Les travaux à venir devraient être axés sur le développement des systèmes de transport avant l'hospitalisation et entre les établissements, le renforcement des hôpitaux de district et l'augmentation du soutien aux centres régionaux.

Acute care surgery in Rwanda: Operative epidemiology and geographic variations in access to care.

BACKGROUND: Surgical management of emergent, life-threatening diseases is an important public health priority. The objectives of this study were to (1) describe acute care general surgery procedures performed at the largest referral hospital in Rwanda and (2) understand the geographic distribution of disease presentations and referral patterns. METHODS: We performed a retrospective review of prospectively collected acute care surgery cases performed at the Centre Hospitalier Universitaire de Kigali (CHUK) in Rwanda between June 1 and December 1, 2011. Using Pearson's χ(2) test and the Fisher exact test, we compared cases originating from within Kigali and transfers from other provinces. Geospatial analyses also were used to further describe transfer patterns. RESULTS: During the study period, 2,758 surgical interventions were performed, of which 25.6% (707/2,758) were general surgery operations. Of these, 45.4% (321/707) met the definition of acute care surgery. Only about one-third-32.3% (92/285)-of patients resided within Kigali, whereas about two-thirds-67.7% (193/285)-were transferred from other provinces. Most patients transferred from other provinces were younger than 18 years of age (40.4%; 78/193), and 83.0% (39/47) of patients older than 50 years of age originated from outside of Kigali. Specific operative indications and surgical procedures varied substantially between patients from Kigali and patients transferred from other provinces. CONCLUSION: Emergency surgical conditions remain important contributors to the global burden of disease, particularly in low- and middle-income countries. Geographic variations exist in terms of operative diagnoses and procedures, which implies a need for improved access to surgical care at the district level with defined transfer mechanisms to greater-level care facilities when needed.

Gram negative bacteria increase non-small cell lung cancer metastasis via Toll-like receptor 4 activation and mitogen-activated protein kinase phosphorylation.

Surgery is required for the curative treatment of lung cancer but is associated with high rates of postoperative pneumonias predominantly caused by gram negative bacteria. Recent evidence suggests that these severe infectious complications may decrease long term survival after hospital discharge via cancer recurrence, but the mechanism is unclear. Lung cancer cells have recently been demonstrated to express Toll-like receptors (TLR) that mediate pathogen recognition. We hypothesized that incubation of non-small cell lung cancer (NSCLC) cells with heat-inactivated Escherichia coli can augment cancer cell adhesion, migration and metastasis via TLR4 signaling. Incubation of murine and human NSCLC cells with E. coli increased in vitro cell adhesion to collagen I, collagen IV and fibronectin, and enhanced in vitro migration. Using hepatic intravital microscopy, we demonstrated that NSCLC cells have increased in vivo adhesion to hepatic sinusoids after coincubation with gram negative bacteria. These enhanced cell adhesion and migration phenotypes following incubation with E. coli were attenuated at three levels: inhibition of TLR4 (Eritoran), p38 MAPK (BIRB0796) and ERK1/2 phosphorylation (PD184352). Incubation of murine NSCLC cells in vitro with E. coli prior to intrasplenic injection significantly augmented formation of in vivo hepatic metastases 2 weeks later. This increase was abrogated by NSCLC TLR4 blockade using Eritoran. TLR4 represents a potential therapeutic target to help prevent severe postoperative infection driven cancer metastasis.

Functional outcomes and quality of life after proximal gastrectomy with esophagogastrostomy using a narrow gastric conduit.

BACKGROUND: The best surgical approach for tumors of the proximal stomach remains controversial. For proximal gastrectomy (PG), the evidence regarding quality of life (QoL) and functional outcomes is controversial. Moreover, there are limited data from non-Asian settings. METHODS: All patients who underwent PG from September 2005 to July 2013 were identified from an institutional database. Demographic, perioperative and pathologic characteristics were retrieved. Symptom scores (0 = best/4 = worst) for reflux symptoms, dysphagia and validated QoL metrics (FACT scale, where a higher score is better) were assessed during early and late follow-up. Eligible patients for analysis were those with no evidence of recurrence. RESULTS: Of 465 upper gastrointestinal cancer resections, 50 were PG for adenocarcinoma (42; 84%), neuroendocrine carcinoma (5; 10%) or other pathologies (3; 6%). R0 resection was achieved in 44 (89.8%) of 49 patients with malignant tumors. Median lymph node collection was 32 (range 7-57). QoL scores did not differ from preoperative to early follow-up but increased compared to both at late follow-up [preoperative, 125 (interquartile range 105-140); early follow-up, 122.5 (97-142); late follow-up, 147 (132-159); p < 0.05]. At early and late follow-up, 9 (21.4%) of 42 and 10 (33.3%) of 30 patients reported reflux symptoms, but most were mild. Endoscopic signs of esophagitis were found in 7 (29%) of 24 patients, but only two of these reported reflux symptoms. Conversely only three of eight patients with reflux symptoms had esophagitis on endoscopy. CONCLUSIONS: Global QoL is not reduced early after PG, and increases compared to baseline at late follow-up. Although reflux symptoms are reported by a quarter of patients, most are mild, and there is little correlation with esophagitis. PG should remain a viable option in the management of proximal gastric tumors.

Classifying leukemia types with chromatin conformation data.

BACKGROUND: Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. RESULTS: Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data. CONCLUSIONS: Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes.

Diagnostic accuracy and utility of intraoperative microscopic margin analysis of gastric and esophageal adenocarcinoma.

BACKGROUND: Positive resection margins are amongst the strongest predictors of cancer-related mortality for adenocarcinoma of the stomach and esophagus. Although intraoperative pathology consultation with frozen section of margins can predict final permanent section pathology, the accuracy of this approach is not known. We sought to determine the diagnostic accuracy of frozen section margin analysis in esophagogastric adenocarcinoma and the impact that it had on surgical therapy. METHODS: Patients with resection of esophagogastric adenocarcinoma at a single centre from 1998 to 2008 were identified. Clinicopathologic data were collected. Frozen section results were compared to permanent section assessment, and sensitivity, specificity, positive, and negative predictive values were calculated. Patients with positive margins by frozen section were reviewed to assess the impact on surgical decision-making. RESULTS: Of 220 patients who underwent surgery for adenocarcinoma of the esophagus and stomach (esophagus: 34/220, EGJ: 106/220, stomach 80/220), 56 % had an intraoperative consultation. Of these 122 patients, 66 % underwent frozen section. All errors on frozen section occurred on the interpretation of the proximal margin. The diagnostic accuracy of frozen section at the proximal margin was 93 % with sensitivity = 67 %, specificity = 100 %, positive predictive value = 100 %, and negative predictive value = 91 %. Signet ring cells were present in 83 % of false-negative readings. Surgical management was altered in 10 of the 13 of patients who had a true positive frozen section and 9 of these patients were converted to R0 resections. CONCLUSIONS: Although very specific, negative results on frozen section require greater caution when signet ring cells are present. For esophagogastric adenocarcinoma, frozen section alters management and may increase the rate of complete resection.

Trainees' views of physician workforce policy in Quebec and their impact on career intentions.

BACKGROUND: The physician workforce in Quebec is regulated by a government-controlled plan. Many specialty trainees expressed concerns about securing a position. Our objective was to analyze physicians' employment issues in Quebec and their impact on residents' training in specialty programs. METHODS: We distributed a web-based self-administrated survey to all Quebec residents training in specialty programs to capture data about residents' ability to find employment, career plans and perceptions regarding the workforce policy. Three groups were considered: graduates, non-graduating senior residents, and junior residents. RESULTS: The overall response rate was 41.5% (985/2372). 47.3% of graduates did not have a position two months before finishing their training. Among residents without a position, 27.1% of graduates intend to leave Quebec, and 19.6% to complete a fellowship to postpone their start in practice. Overall, 77.9% of respondents believed there are not enough job opportunities for the number of trainees. CONCLUSION: Quebec specialty residents experience significant difficulties obtaining a position in the province and perceive that there are not enough job opportunities, which impacts their career plans and could drive them to complete a fellowship or plan to practice outside the province. Trainees' experience in finding employment needs to be considered in planning the physician workforce.

Hox in motion: tracking HoxA cluster conformation during differentiation.

Three-dimensional genome organization is an important higher order transcription regulation mechanism that can be studied with the chromosome conformation capture techniques. Here, we combined chromatin organization analysis by chromosome conformation capture-carbon copy, computational modeling and epigenomics to achieve the first integrated view, through time, of a connection between chromatin state and its architecture. We used this approach to examine the chromatin dynamics of the HoxA cluster in a human myeloid leukemia cell line at various stages of differentiation. We found that cellular differentiation involves a transient activation of the 5'-end HoxA genes coinciding with a loss of contacts throughout the cluster, and by specific silencing at the 3'-end with H3K27 methylation. The 3D modeling of the data revealed an extensive reorganization of the cluster between the two previously reported topologically associated domains in differentiated cells. Our results support a model whereby silencing by polycomb group proteins and reconfiguration of CTCF interactions at a topologically associated domain boundary participate in changing the HoxA cluster topology, which compartmentalizes the genes following differentiation.

Lipopolysaccharide-induced toll-like receptor 4 signaling enhances the migratory ability of human esophageal cancer cells in a selectin-dependent manner.

BACKGROUND: Esophageal cancer is an aggressive malignancy, and emerging data suggest that postoperative infections may promote cancer progression. Systemic exposure to lipopolysaccharide (LPS), a Gram-negative bacterial antigen involved in such infections, has been shown to increase cancer cell adhesion to the hepatic sinusoids in vivo. We investigated the direct impact of LPS on the migratory ability of esophageal cancer cells via the LPS receptor toll-like receptor 4 (TLR4). METHODS: Human esophageal squamous carcinoma cell lines and immortalized normal esophageal mucosa cells were tested for TLR4 surface expression by reverse transcription polymerase chain reaction (RT-PCR) and flow cytometry. TLR4 signaling in response to LPS stimulation was tested in these cells by measuring p38 MAP kinase phosphorylation on Western blot. The impact of TLR4 signaling was measured by static adhesion assays in vitro and on early in vivo migration by intravital microscopy of the liver. RESULTS: Upon LPS stimulation, phosphorylation of p38 was detected in the human esophageal cancer cells HKESC-2. Also, LPS-stimulated HKESC-2 cells showed a twofold increased adhesion to fibronectin and to hepatic sinusoidal endothelium. These effects were abolished by TLR4 inhibition using the small-molecule inhibitor eritoran. Adhesion to fibronectin and hepatic sinusoidal endothelium was also diminished by blockade of p38 phosphorylation and inhibitors of selectin-selectin ligand binding. CONCLUSION: LPS can increase the migratory ability of human esophageal cancer cells by increasing their adhesive properties through TLR4 signaling and selectin ligands. TLR4, p38, and selectin blockade may therefore prove to be a new therapeutic strategy for this aggressive malignancy.

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.

BACKGROUND: Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mechanism of gene expression regulation. Chromosome Conformation Capture Carbon Copy (5C) and its variant Hi-C are techniques used to measure the interaction frequency (IF) between specific regions of the genome. Our goal is to use the IF data generated by these experiments to computationally model and analyze three-dimensional chromatin organization. RESULTS: We formulate a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC) approach called MCMC5C to generate a representative sample from the posterior distribution over structures from IF data. Structures produced from parallel MCMC runs on the same dataset demonstrate that our MCMC method mixes quickly and is able to sample from the posterior distribution of structures and find subclasses of structures. Structural properties (base looping, condensation, and local density) were defined and their distribution measured across the ensembles of structures generated. We applied these methods to a biological model of human myelomonocyte cellular differentiation and identified distinct chromatin conformation signatures (CCSs) corresponding to each of the cellular states. We also demonstrate the ability of our method to run on Hi-C data and produce a model of human chromosome 14 at 1Mb resolution that is consistent with previously observed structural properties as measured by 3D-FISH. CONCLUSIONS: We believe that tools like MCMC5C are essential for the reliable analysis of data from the 3C-derived techniques such as 5C and Hi-C. By integrating complex, high-dimensional and noisy datasets into an easy to interpret ensemble of three-dimensional conformations, MCMC5C allows researchers to reliably interpret the result of their assay and contrast conformations under different conditions. AVAILABILITY: http://Dostielab.biochem.mcgill.ca.