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Utility Analyses of AVITI Sequencing Chemistry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590136. [PMID: 38712138 PMCID: PMC11071311 DOI: 10.1101/2024.04.18.590136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
BACKGROUND DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and transcriptome sequencing of various organisms. Nevertheless, challenges with accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. RESULTS Here, we conduct a comparative analysis using matched DNA and RNA short-reads assays between Element Biosciences AVITI chemistry and Illumina NextSeq 550. Similar comparisons were evaluated for synthetic long-read sequencing for RNA and targeted single-cell transcripts between the AVITI and Illumina NovaSeq 6000. For both DNA and RNA short-read applications, the study found that the AVITI produced significantly higher per sequence quality scores. For PCR-free DNA libraries, we observed up to a 10-fold lower experimentally determined error rate for using the AVITI chemistry compared to the NextSeq 550. For short-read RNA quantification, both AVITI and the NextSeq 550 demonstrated comparable accuracy. With regards to synthetic long-read mRNA and targeted synthetic long read single cell mRNA sequencing, both platforms respective chemistries performed comparably in quantification of genes and isoforms. The AVITI displayed a marginally lower error rate for long reads, with fewer chemistry-specific errors and a higher mutation detection rate. CONCLUSION These results point to the potential of the AVITI platform as a competitive candidate in high-throughput short read sequencing analyses when juxtaposed with the Illumina NextSeq 550.
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Green turtle population recovery at Aldabra Atoll continues after 50 yr of protection. ENDANGER SPECIES RES 2022. [DOI: 10.3354/esr01174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Green turtles Chelonia mydas have been subject to high levels of anthropogenic exploitation, with harvesting at their nesting sites especially pronounced throughout the late 19th and early 20th centuries, leading to worldwide declines. Due to their delayed sexual maturity, long-term protection and monitoring is crucial to allow and accurately demonstrate population recovery. Subsequent to their exploitation, Aldabra Atoll (Republic of Seychelles) has offered the longest continuous protection for nesting green turtles anywhere in the Western Indian Ocean, beginning in 1968. Here, we document the continuing recovery of that population by estimating clutch production within 12 mo nesting seasons over 50 yr of monitoring. An estimated mean of 15297 clutches were laid annually between December 2014 and November 2019. This represents an increase of 173% since Aldabra’s intensive monitoring programme was initiated in 1980, and 410-�665% since 1968. Clutch number increases were recorded at all but 1 of 6 monitored beach groups around the atoll but were most pronounced at Settlement Beach, where exploitation of nesting females was historically most intense. Seasonality data since 2000 showed a year-round nesting season, with elevated activity in April-June peaking on average in May, and a potential shift to later in the year over time. This study highlights the considerable contribution of Aldabra Atoll to regional green turtle numbers and the benefit of long-term protection and monitoring at what can be considered a global reference site for this species.
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2021 Canadian Surgery Forum01. Design and validation of a unique endoscopy simulator using a commercial video game03. Is ethnicity an appropriate measure of health care marginalization?: A systematic review and meta-analysis of the outcomes of diabetic foot ulceration in the Aboriginal population04. Racial disparities in surgery — a cross-specialty matched comparison between black and white patients05. Starting late does not increase the risk of postoperative complications in patients undergoing common general surgical procedures06. Ethical decision-making during a health care crisis: a resource allocation framework and tool07. Ensuring stability in surgical training program leadership: a survey of program directors08. Introducing oncoplastic breast surgery in a community hospital09. Leadership development programs for surgical residents: a review of the literature10. Superiority of non-opioid postoperative pain management after thyroid and parathyroid operations: a systematic review and meta-analysis11. Timing of ERCP relative to cholecystectomy in patients with ductal gallstone disease12. A systematic review and meta-analysis of randomized controlled trials comparing intraoperative red blood cell transfusion strategies13. Postoperative outcomes after frail elderly preoperative assessment clinic: a single-institution Canadian perspective14. Selective opioid antagonists following bowel resection for prevention of postoperative ileus: a systematic review and meta-analysis15. Peer-to-peer coaching after bile duct injury16. Laparoscopic median arcuate ligament release: a video abstract17. Retroperitoneoscopic approach to adrenalectomy19. Endoscopic Zenker diverticulotomy: a video abstract20. Variability in surgeons’ perioperative management of pheochromocytomas in Canada21. The contribution of surgeon and hospital variation in transfusion practice to outcomes for patients undergoing elective gastrointestinal cancer surgery: a population-based analysis22. Perioperative transfusions for gastroesophageal cancers: risk factors and short- and long-term outcomes23. The association between frailty and time alive and at home after cancer surgery among older adults: a population-based analysis24. Psychological and workplace-related effects of providing surgical care during the COVID-19 pandemic in British Columbia, Canada25. Safety of venous thromboembolism prophylaxis in endoscopic retrograde cholangiopancreatography: a systematic review26. Complications and reintervention following laparoscopic subtotal cholecystectomy: a systematic review and meta-analysis27. Synchronization of pupil dilations correlates with team performance in a simulated laparoscopic team coordination task28. Receptivity to and desired design features of a surgical peer coaching program: an international survey9. Impact of the COVID-19 pandemic on rates of emergency department utilization due to general surgery conditions30. The impact of the current COVID-19 pandemic on the exposure of general surgery trainees to operative procedures31. Association between academic degrees and research productivity: an assessment of academic general surgeons in Canada32. Laparoscopic endoscopic cooperative surgery (LECS) for subepithelial gastric lesion: a video presentation33. Effect of the COVID-19 pandemic on acute care general surgery at an academic Canadian centre34. Opioid-free analgesia after outpatient general surgery: a pilot randomized controlled trial35. Impact of neoadjuvant immunotherapy or targeted therapies on surgical resection in patients with solid tumours: a systematic review and meta-analysis37. Surgical data recording in the operating room: a systematic review of modalities and metrics38. Association between nonaccidental trauma and neighbourhood socioeconomic status during the COVID-19 pandemic: a retrospective analysis39. Laparoscopic repair of a transdiaphragmatic gastropleural fistula40. Video-based interviewing in medicine: a scoping review41. Indocyanine green fluorescence angiography for prevention of anastomotic leakage in colorectal surgery: a cost analysis from the hospital payer’s perspective43. Perception or reality: surgical resident and faculty assessments of resident workload compared with objective data45. When illness and loss hit close to home: Do health care providers learn how to cope?46. Remote video-based suturing education with smartphones (REVISE): a randomized controlled trial47. The evolving use of robotic surgery: a population-based analysis48. Prophylactic retromuscular mesh placement for parastomal hernia prevention: a retrospective cohort study of permanent colostomies and ileostomies49. Intracorporeal versus extracorporeal anastomosis in laparoscopic right hemicolectomy: a retrospective cohort study on anastomotic complications50. A lay of the land — a description of Canadian academic acute care surgery models51. Emergency general surgery in Ontario: interhospital variability in structures, processes and models of care52. Trauma 101: a virtual case-based trauma conference as an adjunct to medical education53. Assessment of the National Surgical Quality Improvement Program Surgical Risk Calculator for predicting patient-centred outcomes of emergency general surgery patients in a Canadian health care system54. Sustainability of a narcotic reduction initiative: 1 year following the Standardization of Outpatient Procedure (STOP) Narcotics Study55. Barriers to transanal endoscopic microsurgery referral56. Geospatial analysis of severely injured rural patients in a geographically complex landscape57. Implementation of an incentive spirometry protocol in a trauma ward: a single-centre pilot study58. Impostor phenomenon is a significant risk factor for burnout and anxiety in Canadian resident physicians: a cross-sectional survey59. Understanding the influence of perioperative education on performance among surgical trainees: a single-centre experience60. The effect of COVID-19 pandemic on current and future endoscopic personal protective equipment practices: a national survey of 77 endoscopists61. Case report: delayed presentation of perforated sigmoid diverticulitis as necrotizing infection of the lower limb62. Investigating disparities in surgical outcomes in Canadian Indigenous populations63. Fundoplication is superior to medical therapy for Barrett esophagus disease regression and progression: a systematic review and meta-analysis64. Development of a novel online general surgery learning platform and a qualitative preimplementation analysis65. Hagfish slime exudate as a potential novel hemostatic agent: developing a standardized assessment protocol66. The effect of the first wave of the COVID-19 pandemic on surgical oncology case volumes and wait times67. Safety of same-day discharge in high-risk patients undergoing ambulatory general surgery68. External validation of the Codman score in colorectal surgery: a pragmatic tool to drive quality improvement69. Improved morbidity and gastrointestinal restoration rates without compromising survival rates for diverting loop ileostomy with colonic lavage versus total abdominal colectomy for fulminant Clostridioides difficile colitis: a multicentre retrospective cohort study70. Potential access to emergency general surgical care in Ontario71. Immersive virtual reality (iVR) improves procedural duration, task completion and accuracy in surgical trainees: a systematic review01. Clinical validation of the Canada Lymph Node Score for endobronchial ultrasound02. Venous thromboembolism in surgically treated esophageal cancer patients: a provincial population-based study03. Venous thromboembolism in surgically treated lung cancer patients: a population-based study04. Is frailty associated with failure to rescue after esophagectomy? A multi-institutional comparative analysis of outcomes05. Routine systematic sampling versus targeted sampling of lymph nodes during endobronchial ultrasound: a feasibility randomized controlled trial06. Gastric ischemic conditioning reduces anastomotic complications in patients undergoing esophagectomy: a systematic review and meta-analysis07. Move For Surgery, a novel preconditioning program to optimize health before thoracic surgery: a randomized controlled trial08. In case of emergency, go to your nearest emergency department — Or maybe not?09. Does preoperative SABR increase the risk of complications from lung cancer resection? A secondary analysis of the MISSILE trial10. Segmental resection for lung cancer: the added value of near-infrared fluorescence mapping diminishes with surgeon experience11. Toward competency-based continuing professional development for practising surgeons12. Stereotactic body radiotherapy versus surgery in older adults with NSCLC — a population-based, matched analysis of long-term dependency outcomes13. Role of adjuvant therapy in esophageal cancer patients after neoadjuvant therapy and curative esophagectomy: a systematic review and meta-analysis14. Evaluation of population characteristics on the incidence of thoracic empyema: an ecological study15. Determining the optimal stiffness colour threshold and stiffness area ratio cut-off for mediastinal lymph node staging using EBUS elastography and AI: a pilot study16. Quality assurance on the use of sequential compression stockings in thoracic surgery (QUESTs)17. The relationship between fissureless technique and prolonged air leak for patients undergoing video-assisted thoracoscopic lobectomy18. CXCR2 inhibition as a candidate for immunomodulation in the treatment of K-RAS-driven lung adenocarcinoma19. Assessment tools for evaluating competency in video-assisted thoracoscopic lobectomy: a systematic review20. Understanding the current practice on chest tube management following lung resection among thoracic surgeons across Canada21. Effect of routine jejunostomy tube insertion in esophagectomy: a systematic review and meta-analysis22. Recurrence of primary spontaneous pneumothorax following bullectomy with pleurodesis or pleurectomy: a retrospective analysis23. Surgical outcomes following chest wall resection and reconstruction24. Outcomes following surgical management of primary mediastinal nonseminomatous germ cell tumours25. Does robotic approach offer better nodal staging than thoracoscopic approach in anatomical resection for non–small cell lung cancer? A single-centre propensity matching analysis26. Competency assessment for mediastinal mass resection and thymectomy: design and Delphi process27. The contemporary significance of venous thromboembolism (deep venous thrombosis [DVT] and pulmonary embolus [PE]) in patients undergoing esophagectomy: a prospective, multicentre cohort study to evaluate the incidence and clinical outcomes of VTE after major esophageal resections28. Esophageal cancer: symptom severity at the end of life29. The impact of pulmonary artery reconstruction on postoperative and oncologic outcomes: a systematic review30. Association with surgical technique and recurrence after laparoscopic repair of paraesophageal hernia: a single-centre experience31. Enhanced recovery after surgery (ERAS) in esophagectomy32. Surgical treatment of esophageal cancer: trends in surgical approach and early mortality at a single institution over the past 18 years34. Adverse events and length of stay following minimally invasive surgery in paraesophageal hernia repair35. Long-term symptom control comparison of Dor and Nissen fundoplication following laparoscopic para-esophageal hernia repair: a retrospective analysis36. Willingness to pay: a survey of Canadian patients’ willingness to contribute to the cost of robotic thoracic surgery37. Radiomics in early-stage lung adenocarcinoma: a prediction tool for tumour immune microenvironments38. Effectiveness of intraoperative pyloric botox injection during esophagectomy: how often is endoscopic intervention required?39. An artificial intelligence algorithm for predicting lymph node malignancy during endobronchial ultrasound40. The effect of major and minor complications after lung surgery on length of stay and readmission41. Measuring cost of adverse events following thoracic surgery: a scoping review42. Laparoscopic paraesophageal hernia repair: characterization by hospital and surgeon volume and impact on outcomes43. NSQIP 5-Factor Modified Frailty Index predicts morbidity but not mortality after esophagectomy44. Trajectory of perioperative HRQOL and association with postoperative complications in thoracic surgery patients45. Variation in treatment patterns and outcomes for resected esophageal cancer at designated thoracic surgery centres46. Patient-reported pretreatment health-related quality of life (HRQOL) predicts short-term survival in esophageal cancer patients47. Analgesic efficacy of surgeon-placed paravertebral catheters compared with thoracic epidural analgesia after Ivor Lewis esophagectomy: a retrospective noninferiority study48. Rapid return to normal oxygenation after lung surgery49. Examination of local and systemic inflammatory changes during lung surgery01. Implications of near-infrared imaging and indocyanine green on anastomotic leaks following colorectal surgery: a systematic review and meta-analysis02. Repeat preoperative endoscopy after regional implementation of electronic synoptic endoscopy reporting: a retrospective comparative study03. Consensus-derived quality indicators for operative reporting in transanal endoscopic surgery (TES)04. Colorectal lesion localization practices at endoscopy to facilitate surgical and endoscopic planning: recommendations from a national consensus Delphi process05. Black race is associated with increased mortality in colon cancer — a population-based and propensity-score matched analysis06. Improved survival in a cohort of patients 75 years and over with FIT-detected colorectal neoplasms07. Laparoscopic versus open loop ileostomy reversal: a systematic review and meta-analysis08. Posterior mesorectal thickness as a predictor of increased operative time in rectal cancer surgery: a retrospective cohort study09. Improvement of colonic anastomotic healing in mice with oral supplementation of oligosaccharides10. How can we better identify patients with rectal bleeding who are at high risk of colorectal cancer?11. Assessment of long-term bowel dysfunction in rectal cancer survivors: a population-based cohort study12. Observational versus antibiotic therapy for acute uncomplicated diverticulitis: a noninferiority meta-analysis based on a Delphi consensus13. Radiotherapy alone versus chemoradiotherapy for stage I anal squamous cell carcinoma: a systematic review and meta-analysis14. Is the Hartmann procedure for diverticulitis obsolete? National trends in colectomy for diverticulitis in the emergency setting from 1993 to 201515. Sugammadex in colorectal surgery: a systematic review and meta-analysis16. Sexuality and rectal cancer treatment: a qualitative study exploring patients’ information needs and expectations on sexual dysfunction after rectal cancer treatment17. Video-based interviews in selection process18. Impact of delaying colonoscopies during the COVID-19 pandemic on colorectal cancer detection and prevention19. Opioid use disorder associated with increased anastomotic leak and major complications after colorectal surgery20. Effectiveness of a rectal cancer education video on patient expectations21. Robotic-assisted rectosigmoid and rectal cancer resection: implementation and early experience at a Canadian tertiary centre22. An online educational app for rectal cancer survivors with low anterior resection syndrome: a pilot study23. The effects of surgeon specialization on the outcome of emergency colorectal surgery24. Outcomes after colorectal cancer resections in octogenarians and older in a regional New Zealand setting — What are the predictors of mortality?25. Long-term outcomes after seton placement for perianal fistulae with and without Crohn disease26. A survey of patient and surgeon preference for early ileostomy closure following restorative proctectomy for rectal cancer — Why aren’t we doing it?27. Crohn disease independently associated with longer hospital admission after surgery28. Short-stay (≤ 1 d) diverting loop ileostomy closure can be selectively implemented without an increase in readmission and complication rates: an ACS-NSQIP analysis29. A comparison of perineal stapled rectal prolapse resection and the Altemeier procedure at 2 Canadian academic hospitals30. Mental health and substance use disorders predict 90-day readmission and postoperative complications following rectal cancer surgery31. Early discharge after colorectal cancer resection: trends and impact on patient outcomes32. Oral antibiotics without mechanical bowel preparation prior to emergency colectomy reduces the risk of organ space surgical site infections: a NSQIP propensity score matched study33. The impact of robotic surgery on a tertiary care colorectal surgery program, an assessment of costs and short-term outcomes — a Canadian perspective34. Should we scope beyond the age limit of guidelines? Adenoma detection rates and outcomes of screening and surveillance colonoscopies in patients aged 75–79 years35. Emergency department admissions for uncomplicated diverticulitis: a nationwide study36. Obesity is associated with a complicated episode of acute diverticulitis: a nationwide study37. Green indocyanine angiography for low anterior resection in patients with rectal cancer: a prospective before-and-after study38. The impact of age on surgical recurrence of fibrostenotic ileocolic Crohn disease39. A qualitative study to explore the optimal timing and approach for the LARS discussion01. Racial, ethnic and socioeconomic disparities in diagnosis, treatment and survival of patients with breast cancer: a SEER-based population analysis02. First-line palliative chemotherapy for esophageal and gastric cancer: practice patterns and outcomes in the general population03. Frailty as a predictor for postoperative outcomes following pancreaticoduodenectomy04. Synoptic electronic operative reports identify practice variation in cancer surgery allowing for directed interventions to decrease variation05. The role of Hedgehog signalling in basal-like breast cancer07. Clinical and patient-reported outcomes in oncoplastic breast conservation surgery from a single surgeon’s practice in a busy community hospital in Canada08. Upgrade rate of atypical ductal hyperplasia: 10 years of experience and predictive factors09. Time to first adjuvant treatment after oncoplastic breast reduction10. Preparing to survive: improving outcomes for young women with breast cancer11. Opioid prescription and consumption in patients undergoing outpatient breast surgery — baseline data for a quality improvement initiative12. Rectal anastomosis and hyperthermic intraperitoneal chemotherapy: Should we avoid diverting loop ileostomy?13. Delays in operative management of early-stage, estrogen-receptor positive breast cancer during the COVID-19 pandemic — a multi-institutional matched historical cohort study14. Opioid prescribing practices in breast oncologic surgery15. Oncoplastic breast reduction (OBR) complications and patient-reported outcomes16. De-escalating breast cancer surgery: Should we apply quality indicators from other jurisdictions in Canada?17. The breast cancer patient experience of telemedicine during COVID-1918. A novel ex vivo human peritoneal model to investigate mechanisms of peritoneal metastasis in gastric adenocarcinoma (GCa)19. Preliminary uptake and outcomes utilizing the BREAST-Q patient-reported outcomes questionnaire in patients following breast cancer surgery20. Routine elastin staining improves detection of venous invasion and enhances prognostication in resected colorectal cancer21. Analysis of exhaled volatile organic compounds: a new frontier in colon cancer screening and surveillance22. A clinical pathway for radical cystectomy leads to a shorter hospital stay and decreases 30-day postoperative complications: a NSQIP analysis23. Fertility preservation in young breast cancer patients: a population-based study24. Investigating factors associated with postmastectomy unplanned emergency department visits: a population-based analysis25. Impact of patient, tumour and treatment factors on psychosocial outcomes after treatment in women with invasive breast cancer26. The relationship between breast and axillary pathologic complete response in women receiving neoadjuvant chemotherapy for breast cancer01. The association between bacterobilia and the risk of postoperative complications following pancreaticoduodenectomy02. Surgical outcome and quality of life following exercise-based prehabilitation for hepatobiliary surgery: a systematic review and meta-analysis03. Does intraoperative frozen section and revision of margins lead to improved survival in patients undergoing resection of perihilar cholangiocarcinoma? A systematic review and meta-analysis04. Prolonged kidney procurement time is associated with worse graft survival after transplantation05. Venous thromboembolism following hepatectomy for colorectal metastases: a population-based retrospective cohort study06. Association between resection approach and transfusion exposure in liver resection for gastrointestinal cancer07. The association between surgeon volume and use of laparoscopic liver resection for gastrointestinal cancer08. Immune suppression through TIGIT in colorectal cancer liver metastases09. “The whole is greater than the sum of its parts” — a combined strategy to reduce postoperative pancreatic fistula after pancreaticoduodenectomy10. Laparoscopic versus open synchronous colorectal and hepatic resection for metastatic colorectal cancer11. Identifying prognostic factors for overall survival in patients with recurrent disease following liver resection for colorectal cancer metastasis12. Modified Blumgart pancreatojejunostomy with external stenting in laparoscopic Whipple reconstruction13. Laparoscopic versus open pancreaticoduodenectomy: a single centre’s initial experience with introduction of a novel surgical approach14. Neoadjuvant chemotherapy versus upfront surgery for borderline resectable pancreatic cancer: a single-centre cohort analysis15. Thermal ablation and telemedicine to reduce resource utilization during the COVID-19 pandemic16. Cost-utility analysis of normothermic machine perfusion compared with static cold storage in liver transplantation in the Canadian setting17. Impact of adjuvant therapy on overall survival in early-stage ampullary cancers: a single-centre retrospective review18. Presence of biliary anaerobes enhances response to neoadjuvant chemotherapy in pancreatic ductal adenocarcinoma19. How does tumour viability influence the predictive capability of the Metroticket model? Comparing predicted-to-observed 5-year survival after liver transplant for hepatocellular carcinoma20. Does caudate resection improve outcomes in patients undergoing curative resection for perihilar cholangiocarcinoma? A systematic review and meta-analysis21. Appraisal of multivariable prognostic models for postoperative liver decompensation following partial hepatectomy: a systematic review22. Predictors of postoperative liver decompensation events following resection in patients with cirrhosis and hepatocellular carcinoma: a population-based study23. Characteristics of bacteriobilia and impact on outcomes after Whipple procedure01. Inverting the y-axis: the future of MIS abdominal wall reconstruction is upside down02. Progressive preoperative pneumoperitoneum: a single-centre retrospective study03. The role of radiologic classification of parastomal hernia as a predictor of the need for surgical hernia repair: a retrospective cohort study04. Comparison of 2 fascial defect closure methods for laparoscopic incisional hernia repair01. Hypoalbuminemia predicts serious complications following elective bariatric surgery02. Laparoscopic adjustable gastric band migration inducing jejunal obstruction associated with acute pancreatitis: aurgical approach of band removal03. Can visceral adipose tissue gene expression determine metabolic outcomes after bariatric surgery?04. Improvement of kidney function in patients with chronic kidney disease and severe obesity after bariatric surgery: a systematic review and meta-analysis05. A prediction model for delayed discharge following gastric bypass surgery06. Experiences and outcomes of Indigenous patients undergoing bariatric surgery: a mixed-methods scoping review07. What is the optimal common channel length in revisional bariatric surgery?08. Laparoscopic management of internal hernia in a 34-week pregnant woman09. Characterizing timing of postoperative complications following elective Roux-en-Y gastric bypass and sleeve gastrectomy10. Canadian trends in bariatric surgery11. Common surgical stapler problems and how to correct them12. Management of choledocholithiasis following Roux-en-Y gastric bypass: a systematic review and meta-analysis. Can J Surg 2021; 64:S80-S159. [PMID: 35483046 PMCID: PMC8677574 DOI: 10.1503/cjs.021321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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548 “The New Normal”? How We Adapted Simulation Training in The Midst of the Coronavirus Pandemic. Br J Surg 2021. [PMCID: PMC8135871 DOI: 10.1093/bjs/znab135.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Introduction
Delivering high quality teaching during an international pandemic is challenging but becomes increasingly important when trainees are taking on new roles and responsibilities. Instead of ceasing our simulation programme, we adapted it to comply with local infection control guidelines. We devised in-situ high-fidelity ward round simulations for all levels of trainee, from newly qualified doctors to senior registrars.
Method
The ward round consisted of three simulated patients with a range of conditions appropriate for the level of trainee, role-played by faculty members. The simulations were offered to all Foundation Year Doctors, Junior Middle Grade Doctors and Surgical Speciality Trainees with all participants wearing Personal Protective Equipment (PPE) according to COVID-19 infection control policy.
Results
A total of 81 trainees took part in the simulations. Almost all reported it as ‘very useful’ and that it improved confidence in progressing to the next stage of their career. Trainees also found it enjoyable and that personalised feedback allowed them to identify areas for development.
Conclusions
We have shown that ward round simulations can be run safely and effectively despite current COVID-19 restrictions. Even senior trainees found that a ward round simulation was useful and were keen to see it become a regular part of deanery teaching.
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550 “No One Told Me About This Side of The Job!” A Novel Method for Teaching Senior Surgical Trainees. Br J Surg 2021. [DOI: 10.1093/bjs/znab134.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Introduction
Higher surgical training is specifically geared towards preparation for working as a Consultant, but trainees typically get limited exposure to Consultant level administration tasks. Whilst Consultants are familiar with these tasks, registrars are often naïve to this side of clinical practice and new Consultants find it takes up a significant proportion of their time. We developed an “office admin” simulation session as a method for gaining further non-technical skills in surgery.
Method
A simulation based on a real Consultant General Surgeon’s workload was created, which included actioning pathology reports, vetting referrals, and planning a theatre list. Trainees were given 40 minutes to work through the tasks before debriefing with an experienced simulation facilitator.
Results
Six general surgical trainees took part in the pilot. All found it ‘useful’ or ‘very useful’ and stated that it will help prepare them for the role of Consultant. All felt it would make a useful regular addition to the regional teaching programme.
Conclusions
This novel simulation was well received and demonstrated a useful method to practise these skills in preparing for the role of Consultant. We aim to develop the simulation package further so it can augment the regional speciality training.
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Temperature limits to deep subseafloor life in the Nankai Trough subduction zone. Science 2020; 370:1230-1234. [PMID: 33273103 DOI: 10.1126/science.abd7934] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023]
Abstract
Microorganisms in marine subsurface sediments substantially contribute to global biomass. Sediments warmer than 40°C account for roughly half the marine sediment volume, but the processes mediated by microbial populations in these hard-to-access environments are poorly understood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120°C hot sediments in the Nankai Trough subduction zone. Above 45°C, concentrations of vegetative cells drop two orders of magnitude and endospores become more than 6000 times more abundant than vegetative cells. Methane is biologically produced and oxidized until sediments reach 80° to 85°C. In 100° to 120°C sediments, isotopic evidence and increased cell concentrations demonstrate the activity of acetate-degrading hyperthermophiles. Above 45°C, populated zones alternate with zones up to 192 meters thick where microbes were undetectable.
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A pan-Canadian prospective study of young women with breast cancer: the rationale and protocol design for the RUBY study. Curr Oncol 2020; 27:e516-e523. [PMID: 33173392 PMCID: PMC7606039 DOI: 10.3747/co.27.6751] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Introduction The understanding of the biology and epidemiology of, and the optimal therapeutic strategies for, breast cancer (bca) in younger women is limited. We present the rationale, design, and initial recruitment of Reducing the Burden of Breast Cancer in Young Women (ruby), a unique national prospective cohort study designed to examine the diagnosis, treatment, quality of life, and outcomes from the time of diagnosis for young women with bca. Methods Over a 4-year period at 33 sites across Canada, the ruby study will use a local and virtual recruitment model to enrol 1200 women with bca who are 40 years of age or younger at the time of diagnosis, before initiation of any treatment. At a minimum, comprehensive patient, tumour, and treatment data will be collected to evaluate recurrence and survival. Patients may opt to complete patient-reported questionnaires, to provide blood and tumour samples, and to be contacted for future research, forming the core dataset from which 4 subprojects evaluating genetics, lifestyle factors, fertility, and local management or delivery of care will be performed. Summary The ruby study will be the most comprehensive repository of data, biospecimens, and patient-reported outcomes ever collected with respect to young women with bca from the time of diagnosis, enabling research unique to that population now and into the future. This research model could be used for other oncology settings in Canada.
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Psychosocial outcomes following contralateral prophylactic mastectomy in women with unilateral, nonhereditary breast cancer. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)30642-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hypoglycaemia represents a clinically significant manifestation of PIK3CA- and CCND2-associated segmental overgrowth. Clin Genet 2018; 93:687-692. [PMID: 28941273 DOI: 10.1111/cge.13145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 01/31/2023]
Abstract
The PI3K-AKT signalling cascade has a highly conserved role in a variety of processes including cell growth and glucose homoeostasis. Variants affecting this pathway can lead to one of several segmental overgrowth disorders. These conditions are genetically heterogeneous and require tailored, multidisciplinary involvement throughout life. Hypoglycaemia is common in other overgrowth syndromes but has been described only sporadically in association with PIK3CA and CCND2 variants. We report a cohort of 6 children with megalencephaly-capillary malformation (MCAP) and megalencephaly-polydactyly-polymicrogyria-hydrocephalus (MPPH) syndromes who developed clinically significant hypoglycaemia. Based on our findings, we suggest that segmental overgrowth patients should be screened for low blood glucose levels during childhood and there should be early specialist endocrine review in any children who develop hypoglycaemia.
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Abstract
SDHB mutations are linked to the familial paraganglioma syndrome type 4 (PGL4), which is associated with predominantly extra-adrenal disease and has high metastatic rates. Despite the lower penetrance rates in carriers of SDHB mutations compared to mutations in other paraganglioma susceptibility genes, the aggressive behavior of SDHB-linked disease warrants intensive surveillance to identify and resect tumors early. Patients with similar SDHB genotypes in whom the PGL syndrome manifests often exhibit very heterogeneous phenotypes. Tumors can arise in various locations, and management can be considerably different, depending on tumor site and pathology. We present a case series of five SDHB mutation carriers over four generations from the same family to illustrate the complexities in management.
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Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation. Front Microbiol 2015; 6:1425. [PMID: 26779119 PMCID: PMC4688376 DOI: 10.3389/fmicb.2015.01425] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 11/30/2015] [Indexed: 11/13/2022] Open
Abstract
Hydrothermal vents are an important contributor to marine biogeochemistry, producing large volumes of reduced fluids, gasses, and metals and housing unique, productive microbial and animal communities fueled by chemosynthesis. Methane is a common constituent of hydrothermal vent fluid and is frequently consumed at vent sites by methanotrophic bacteria that serve to control escape of this greenhouse gas into the atmosphere. Despite their ecological and geochemical importance, little is known about the ecophysiology of uncultured hydrothermal vent-associated methanotrophic bacteria. Using metagenomic binning techniques, we recovered and analyzed a near-complete genome from a novel gammaproteobacterial methanotroph (B42) associated with a white smoker chimney in the Southern Lau basin. B42 was the dominant methanotroph in the community, at ∼80x coverage, with only four others detected in the metagenome, all on low coverage contigs (7x–12x). Phylogenetic placement of B42 showed it is a member of the Methylothermaceae, a family currently represented by only one sequenced genome. Metabolic inferences based on the presence of known pathways in the genome showed that B42 possesses a branched respiratory chain with A- and B-family heme copper oxidases, cytochrome bd oxidase and a partial denitrification pathway. These genes could allow B42 to respire over a wide range of oxygen concentrations within the highly dynamic vent environment. Phylogenies of the denitrification genes revealed they are the result of separate horizontal gene transfer from other Proteobacteria and suggest that denitrification is a selective advantage in conditions where extremely low oxygen concentrations require all oxygen to be used for methane activation.
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P-292: Acute geratology wards and stroke patients. Eur Geriatr Med 2015. [DOI: 10.1016/s1878-7649(15)30390-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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P-236: The involvement of older patients in medical student education from the University of Oxford. Eur Geriatr Med 2015. [DOI: 10.1016/s1878-7649(15)30334-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
In 2001, genetic testing for BRCA1 and BRCA2 was introduced in Ontario, for women at high-risk of breast or ovarian cancer. To date over 30,000 individuals have been tested throughout Ontario. Testing was offered to all Ontario residents who were eligible under any of 13 criteria. We report the results of tests conducted at Mount Sinai Hospital from 2007 to 2014. A total of 4726 individuals were tested, 764 (16.2%) were found to carry a pathogenic variant (mutation). Among 3684 women and men who underwent testing without a known familial BRCA mutation, 331 (9.0%) were found to carry a mutation. Among 1042 women and men tested for a known family mutation, 433 (41.6%) were positive. There were 603 female mutation carriers, of these, 303 were affected with breast or ovarian cancer (50%) and 16 with another cancer (2.3%). Of 284 unaffected female carriers, 242 (85%) were tested for a known family mutation and 42 (15%) were the first person in the family to be tested. By placing greater emphasis on recruiting unaffected female relatives of known mutation carriers for testing, greater than one-half of newly identified carriers will be unaffected.
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Large-scale discovery of novel genetic causes of developmental disorders. Nature 2015; 519:223-8. [PMID: 25533962 PMCID: PMC5955210 DOI: 10.1038/nature14135] [Citation(s) in RCA: 773] [Impact Index Per Article: 85.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 12/04/2014] [Indexed: 12/23/2022]
Abstract
Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.
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Prevalence of dental trauma and use of mouthguards in rugby union players. Aust Dent J 2014; 59:473-81. [DOI: 10.1111/adj.12223] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 11/24/2022]
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Functional divergence in gastrointestinal microbiota in physically-separated genetically identical mice. Sci Rep 2014; 4:5437. [PMID: 24961643 PMCID: PMC4069701 DOI: 10.1038/srep05437] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/05/2014] [Indexed: 12/20/2022] Open
Abstract
Despite the fundamental contribution of the gut microbiota to host physiology, the extent of its variation in genetically-identical animals used in research is not known. We report significant divergence in both the composition and metabolism of gut microbiota in genetically-identical adult C57BL/6 mice housed in separate controlled units within a single commercial production facility. The reported divergence in gut microbiota has the potential to confound experimental studies using mammalian models.
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Modes of delivery of genetic testing services and the uptake of cancer risk management strategies in BRCA1 and BRCA2 carriers. Clin Genet 2013; 85:49-53. [PMID: 23438721 DOI: 10.1111/cge.12130] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 02/18/2013] [Accepted: 02/18/2013] [Indexed: 01/23/2023]
Abstract
BRCA testing services are now offered by various healthcare providers, thus it is important to evaluate whether the implementation of cancer risk management (CRM) strategies varies by service provider. Using a registry-based sample of 795 female BRCA mutation carriers, we explored the association between uptake of CRM strategies with duration of genetic counseling (GC) sessions, provider type, and other demographic and clinical variables. All participants completed a baseline questionnaire. Information about uptake of CRM strategies was collected for a subset of 438 participants who completed additional questions. Summary statistics and Pearson chi-squared analysis were used to examine the associations between demographic and clinical variables with service delivery factors and with the uptake of various CRM strategies. Overall uptake of CRM strategies was high across all provider types. However, GC sessions were longer when provided by a genetics professional than by another provider (p < 0.001). Furthermore, higher frequencies of uptake of most CRM strategies were associated with longer GC sessions and when testing was performed by a genetics professional. Identification of factors to optimize delivery of these specialized GC services is important to maximize implementation of CRM strategies in BRCA carriers.
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Development of a Patient Decision Aid for Older Women With Stage I Breast Cancer Considering Adjuvant Treatment Postlumpectomy. Int J Radiat Oncol Biol Phys 2012. [DOI: 10.1016/j.ijrobp.2012.07.573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Identification of patients at high risk of negative psychological consequences associated with BRCA1 mutation. Hered Cancer Clin Pract 2012. [PMCID: PMC3287434 DOI: 10.1186/1897-4287-10-s1-a14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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P5-15-03: Development of a Patient Decision Aid for Women 70 Years and Older with Stage I, Hormonally Sensitive, Breast Cancer Considering Adjuvant Treatment Post-Lumpectomy. Cancer Res 2011. [DOI: 10.1158/0008-5472.sabcs11-p5-15-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Decision Aids (DA) are developed with the intent to support people in making specific and deliberate choices by improving information transfer about different outcomes. Previous research has shown that DAs can increase patient knowledge regarding treatment options, reduce decisional conflict, and increase patient satisfaction with the decision-making process. However, no DAs have been developed to help older breast cancer patients decide whether or not to undergo adjuvant RT. We developed and tested a DA for older women with stage I,ER/PR positive breast cancer considering adjuvant treatment post-lumpectomy and we examined its impact on treatment decision-making process.
Methods and Materials: A DA was developed and evaluated in three steps following the Ottawa Decision Aid Framework: 1) Needs assessment (N=16); 2) Pilot I, to examine the DA's acceptability (N=12); and 3) Pilot II, a pre-test post-test (N=38) with older women with ER/PR responsive breast cancer post-lumpectomy who were receiving adjuvant RT. Measures included questionnaires to assess patient's satisfaction with the DA, patients’ self-reported decisional conflict (DC), level of distress, treatment-related knowledge, and choice predisposition
Results: The DA is a booklet that details each adjuvant treatment option's benefits, risks and side-effects tailored to their clinical profile; includes a value clarification exercise; and steps to guide them towards their own treatment decision. All women felt the DA was helpful and informative. Compared with baseline scores, patients had a statistically significant (p < .05) reduction in DC (adjusted mean difference [AMD], −7.18; 95% confidence interval [CI], −13.50 to 12.59); increased clarity of the treatment benefits and risks (AMD, −10.86, CI, −20.33 to 21.49; and improved general treatment knowledge (AMD, 8.99, CI, 2.88 to 10.28) after using the DA. General trends were also reported in patient's choice predisposition scores suggesting potential differences in treatment decision after DA use. Discussion: This study provides evidence that this DA may be a helpful educational tool for this group of women. The quality of care for older breast cancer patients may be enhanced by using a tailored DA to help the patient be informed of their treatment options and to prepare for decision-making.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-15-03.
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162 The clinical management of relatives of young sudden arrhythmic death victims; icds are rarely indicated. BRITISH HEART JOURNAL 2011. [DOI: 10.1136/heartjnl-2011-300198.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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No clear evidence for an association between GH replacement and relapse of intracranial germ cell tumours: single centre and KIMS experience. Eur J Endocrinol 2010; 163:357-8. [PMID: 20516207 DOI: 10.1530/eje-10-0498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Breast and ovarian cancer risk perception after prophylactic salpingo-oophorectomy due to an inherited mutation in theBRCA1orBRCA2gene. Clin Genet 2009; 75:220-4. [DOI: 10.1111/j.1399-0004.2008.01117.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Novel and recurring ABCA12 mutations associated with harlequin ichthyosis: implications for prenatal diagnosis. Br J Dermatol 2007; 158:611-3. [DOI: 10.1111/j.1365-2133.2007.08277.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Equilibrium surface adsorption behavior in complex anionic/nonionic surfactant mixtures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:10140-9. [PMID: 17725368 DOI: 10.1021/la701151m] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Neutron reflectivity (NR) and small angle neutron scattering (SANS) have been used to investigate the equilibrium surface adsorption behavior and the solution microstructure of mixtures of the anionic surfactant sodium 6-dodecyl benzene-4 sulfonate (SDBS) with the nonionic surfactants monododecyl octaethylene glycol (C12EO8) and monododecyl triiscosaethylene glycol (C12EO23). In the SDBS/C12EO8 and SDBS/C12EO23 solutions, small globular mixed micelles are formed. However, the addition of Ca2+ ions to SDBS/C12EO8 results in a transition to a vesicle phase or a mixed vesicle/micellar phase for SDBS rich compositions. In contrast, this transition hardly exists for the SDBS/C12EO23 mixture, and occurs only in a narrow composition region which is rich in SDBS. The adsorption of the SDBS/C12EO8 mixture at the air-solution interface is in the form of a mixed monolayer, with a composition variation that is not consistent with ideal mixing. In water and in the presence of NaCl, the nonideality can be broadly accounted for by regular solution theory (RST). At solution compositions rich in SDBS, the addition of Ca2+ ions results in the formation of multilayer structures at the interface. The composition range over which multilayer formation exists depends upon the Ca2+ concentration added. In comparison, the addition of a simple monovalent electrolyte, NaCl, at the same ionic strength does not have the same impact upon the adsorption, and the surface structure remains as a monolayer. Correspondingly, in solution, the mixed surfactant aggregates remain as relatively small globular micelles. In the presence of Ca2+ counterions, the variation in surface composition with solution composition is not well described by RST over the entire composition range. Furthermore, the mixing behavior is not strongly correlated with variations in the solution microstructure, as observed in other related systems.
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Supportive-expressive group therapy for women with brca1/2mutations: Results of a phase II trial. Nurs Health Sci 2005. [DOI: 10.1111/j.1442-2018.2005.00233_12.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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29
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Impact of BRCA mutation test results in members of hereditary breast ovarian cancer (HBOC) families. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.1014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Comparison of continuation or cessation of growth hormone (GH) therapy on body composition and metabolic status in adolescents with severe GH deficiency at completion of linear growth. J Clin Endocrinol Metab 2004; 89:3890-5. [PMID: 15292323 DOI: 10.1210/jc.2003-031588] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although GH replacement improves the features of GH deficiency (GHD) in adults, it has yet to be established whether cessation of GH at completion of childhood growth results in adverse consequences for the adolescent with GHD. Effects of continuation or cessation of GH on body composition, insulin sensitivity, and lipid levels were studied in 24 adolescents (13 males, 11 females, aged 17.0 +/- 0.3, yr, mean +/- se, puberty stage 4 or 5) in whom height velocity was less than 2 cm/yr. Provocative testing confirmed severe GHD [peak GH < 9 mU/liter (3 microg/liter)] in all cases and was followed by a lead-in period of 3 months during which the pediatric dose of GH continued unchanged. Baseline investigations were then performed using dual-energy x-ray absorptiometry (body composition), lipid measurements, and assessment of insulin sensitivity by both homeostasis model assessment and a short insulin tolerance test. Twelve patients remained on GH (0.35 U/kg.wk), and 12 patients ceased GH treatment. The groups were followed up in parallel with repeat observations made after 6 and 12 months. No endocrine differences were evident between the groups at baseline. GH cessation resulted in a reduction of serum IGF-I Z score [-1.62 +/- 0.29, baseline vs. -2.52 +/- 0.12, 6 months (P < 0.05) vs. -2.52 +/- 0.10, 12 months (P < 0.01)] but values remained unchanged in those continuing GH replacement. Lean body mass increased by 2.5 +/- 0.5 kg ( approximately 6%) over 12 months in those receiving GH but was unchanged after GH discontinuation. Cessation of GH resulted in increased insulin sensitivity [short insulin tolerance test, 153 +/- 22 micromol/liter.min, baseline vs. 187 +/- 20, 6 months (P < 0.05) vs. 204 +/- 14, 12 months (P = 0.05)], but no significant change was seen during 12 months of GH continuation. Lipid levels remained unaltered in both groups. Continuation of GH at completion of linear growth resulted in ongoing accrual of lean body mass (LBM), whereas skeletal muscle mass remained static after GH cessation in these adolescents with GHD. This divergence of gain in LBM is of potential importance because increases in LBM occur as a feature of healthy late adolescent development. GH is a major mediator of insulin sensitivity, independent of body composition in adolescents. Further studies are required to determine whether discontinuation of GH in the adolescent with severe GHD once linear growth is complete results in long-term irreversible adverse physical and metabolic consequences and to determine conclusively the benefits of continuing GH therapy.
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Using case study comparisons to explore genotype-phenotype correlations in Williams-Beuren syndrome. J Med Genet 2003; 40:136-40. [PMID: 12566524 PMCID: PMC1735363 DOI: 10.1136/jmg.40.2.136] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Risks associated with herbal slimming remedies. THE JOURNAL OF THE ROYAL SOCIETY FOR THE PROMOTION OF HEALTH 2002; 122:213-9. [PMID: 12557729 DOI: 10.1177/146642400212200407] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The market for non-conventional, natural herbal medicines is growing. This marketing opportunity has been seized upon by some unscrupulous practitioners to sell potentially unsafe 'herbal' products. Several people attended a Chinese herbalist for weight loss advice and were sold 'herbal' preparations that contained fenfluramine, a drug which was withdrawn from sale in the West in 1997 after its use was linked to primary pulmonary hypertension and valvular heart disease. Adulteration of Chinese medicines with Western drugs is becoming an increasing problem, and deaths have been reported from Japan and other Far Eastern countries linked to Chinese slimming aids containing N-nitroso-fenfluramine. There is a need for increased public awareness of such risks associated with the use of unlicensed medicines; a system of registration for medical herbalists is also required to protect both the reputable practitioners and the general public.
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Suprasellar germ cell tumours: specific problems and the evolution of optimal management with a combined chemoradiotherapy regimen. Clin Endocrinol (Oxf) 2002; 57:487-500. [PMID: 12354131 DOI: 10.1046/j.1365-2265.2002.01620.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE Suprasellar germ cell tumours are rare, and there are few series of patients outlining the problems in diagnosis and management, and providing clear guidelines for optimal therapy. We have therefore reviewed our own series of 11 such patients who were managed in a joint endocrinology/clinical oncology setting. PATIENTS AND DESIGN A retrospective case review assessment of all patients seen within a given time. Clinical, biochemical and radiological findings were reviewed, the types of therapy administered noted, and the responses to treatment analysed. RESULTS In the years 1977-2001, 11 patients with suprasellar (SS) germ cell tumours (GCT) were seen (germinomatous : nongerminomatous = 8 : 3). SSGCT had an approximately equal sex incidence (M : F, 6 : 5), in contrast to pineal tumours, the commonest site of origin of intracranial GCT and which occur predominantly in men. The median age at presentation was 20 years (range 6-49 years) with a median duration of symptoms before diagnosis of 17 months (range 1-35 months). Polyuria was the commonest presenting symptom (10 patients). Diabetes insipidus occurred in all patients, as did partial or complete anterior pituitary failure. Visual failure was present in 55% of cases. Anorexia, weight loss and disturbed thirst sensation were also common. Positron emission tomography scanning was occasionally useful in the evaluation of suprasellar tumours/pituitary stalk lesions deemed too risky to biopsy. A "central nervous system-friendly" chemoradiotherapy regimen comprising vincristine, etoposide and carboplatin and differential daily dose irradiation, usually administered using a partial transmission block technique, produced a 5-year survival of 100% with low morbidity. Treatment did not correct previously abnormal endocrine function although it did improve vision in three of six patients. CONCLUSIONS We therefore emphasize the use of techniques other than biopsy in the diagnosis of these patients, note the problems in the management of their fluid control, and highlight the favourable response to a combined chemotherapy-radiotherapy protocol.
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Evaluation of the needs of male carriers of mutations in BRCA1 or BRCA2 who have undergone genetic counseling. Am J Hum Genet 2000; 67:1494-504. [PMID: 11063672 PMCID: PMC1287926 DOI: 10.1086/316907] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2000] [Accepted: 10/12/2000] [Indexed: 01/07/2023] Open
Abstract
To date, the concerns of men at risk of inheriting a BRCA1 mutation or a BRCA2 mutation have received little attention. It had been anticipated that few men would be interested in predictive testing when a BRCA mutation was identified in their family. However, these men are often affected emotionally by diagnoses of breast cancer in their relatives and may themselves harbor fears that cancer will develop. Male carriers of BRCA1/2 mutations are at increased risk of development of cancers of several types, including those of the breast and prostate. We conducted an evaluation of the needs and experiences of 59 male carriers of BRCA1/2 mutations followed at either the University of Toronto or Creighton University. We assessed their motivations for seeking genetic counseling and testing, involvement in family discussions of breast and ovarian cancer, risk perception, changes in cancer-screening practices, and overall satisfaction with the genetic-counseling process. The principal motivation for seeking genetic counseling was concern for their daughters. The majority (88%) of men participated in family conversations about breast and ovarian cancer, and 47% participated in conversations about prophylactic surgery. Most men believed that they were at increased risk of development of cancer (prostate, breast, colorectal, and skin cancers). However, fewer than one-half (43%) of the men with no previous diagnosis of cancer stated that their prostate cancer-surveillance practices had changed after they had received genetic test results. More than one-half (55%) had intrusive thoughts about their cancer risk. Although levels of satisfaction were high, practitioners should be aware of (a) potential pressures influencing men to request predictive testing, (b) the difficulties that men encounter in establishing surveillance regimens for breast and prostate cancer, and (c) the general lack of information about men's particular experiences in the medical community.
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Abstract
Supravalvular aortic stenosis (SVAS) is a congenital narrowing of the ascending aorta which can occur sporadically, as an autosomal dominant condition, or as one component of Williams syndrome. SVAS is caused by translocations, gross deletions and point mutations that disrupt the elastin gene (ELN) on 7q11.23. Functional hemizygosity for elastin is known to be the cause of SVAS in patients with gross chromosomal abnormalities involving ELN. However, the pathogenic mechanisms of point mutations are less clear. One hundred patients with diagnosed SVAS and normal karyotypes were screened for mutations in the elastin gene to further elucidate the molecular pathology of the disorder. Mutations associated with the vascular disease were detected in 35 patients, and included nonsense, frameshift, translation initiation and splice site mutations. The four missense mutations identified are the first of this type to be associated with SVAS. Here we describe the spectrum of mutations occurring in familial and sporadic SVAS and attempt to define the mutational mechanisms involved in SVAS. SVAS shows variable penetrance within families but the progressive nature of the disorder in some cases, makes identification of the molecular lesions important for future preventative treatments.
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A transcription factor involved in skeletal muscle gene expression is deleted in patients with Williams syndrome. Eur J Hum Genet 1999; 7:737-47. [PMID: 10573005 DOI: 10.1038/sj.ejhg.5200396] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Williams-Beuren syndrome (WS) is a developmental disorder caused by a hemizygous microdeletion of approximately 1.4MB at chromosomal location 7q11.23. The transcription map of the WS critical region is not yet complete. We have isolated and characterised a 3.4 kb gene, GTF3, which occupies about 140 kb of the deleted region. Northern blot analysis showed that the gene is expressed in skeletal muscle and heart, and RT-PCR analysis showed expression in a range of adult tissues with stronger expression in foetal tissues. Part of the conceptual GTF3 protein sequence is almost identical to a recently reported slow muscle-fibre enhancer binding protein MusTRD1, and shows significant homology to the 90 amino-acid putative helix-loop-helix repeat (HLH) domains of the transcription factor TFII-I (encoded for by the gene GTF2I). These genes may be members of a new family of transcription factors containing this HLH-like repeated motif. Both GTF3 and GTF2I map within the WS deleted region, with GTF2I being positioned distal to GTF3. GTF3 is deleted in patients with classic WS, but not in patients we have studied with partial deletions of the WS critical region who have only supravalvular aortic stenosis. A feature of WS is abnormal muscle fatiguability, and we suggest that haploinsufficiency of the GTF3 gene may be the cause of this.
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39
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Abstract
Williams syndrome (WS) is a contiguous gene syndrome caused by hemizygosity for a chromosomal deletion at 7q11.23. The range of phenotypes includes mental retardation, dysmorphic facies, heart abnormalities, short stature, a specific cognitive profile, hyperacusis, and infantile hypercalcaemia. To identify all the deleted genes, we have constructed a detailed physical map and complete BAC/PAC contig of the critical region, extending a distance of approximately 2 Mb and delimited by the nondeleted markers D7S1816 and D7S489A. Somatic cell hybrids of WS patients were made and used to define the centromeric and telomeric deletion breakpoints, enabling the size of the WS deletion to be defined as approximately 1.4 Mb. Genes previously mapped to the region have been located on the contig, and we have isolated eight transcripts, two of which have been characterized as the genes CPETR1 and CPETR2. This contig and expressed sequence map will form the basis for the construction of a complete transcription map of the deleted region and will enable genotype-phenotype correlations to be attempted to identify the individual components of WS.
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Williams syndrome: use of chromosomal microdeletions as a tool to dissect cognitive and physical phenotypes. Am J Hum Genet 1999; 64:118-25. [PMID: 9915950 PMCID: PMC1377709 DOI: 10.1086/302214] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In Williams syndrome (WS), a deletion of approximately 1.5 Mb on one copy of chromosome 7 causes specific physical, cognitive, and behavioral abnormalities. Molecular dissection of the phenotype may be a route to identification of genes important in human cognition and behavior. Among the genes known to be deleted in WS are ELN (which encodes elastin), LIMK1 (which encodes a protein tyrosine kinase expressed in the developing brain), STX1A (which encodes a component of the synaptic apparatus), and FZD3. Study of patients with deletions or mutations confined to ELN showed that hemizygosity for elastin is responsible for the cardiological features of WS. LIMK1 and STX1A are good candidates for cognitive or behavioral aspects of WS. Here we describe genetic and psychometric testing of patients who have small deletions within the WS critical region. Our results suggest that neither LIMK1 hemizygosity (contrary to a previous report) nor STX1A hemizygosity is likely to contribute to any part of the WS phenotype, and they emphasize the importance of such patients for dissecting subtle but highly penetrant phenotypes.
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Abstract
We have isolated a family of four vertebrate genes homologous to eyes absent (eya), a key regulator of ocular development in Drosophila. Here we present the detailed characterization of the EYA4 gene in human and mouse. EYA4 encodes a 640 amino acid protein containing a highly conserved C-terminal domain of 271 amino acids which in Drosophila eya is known to mediate developmentally important protein-protein interactions. Human EYA4 maps to 6q23 and mouse Eya4 maps to the predicted homology region near the centromere of chromosome 10. In the developing mouse embryo, Eya4 is expressed primarily in the craniofacial mesenchyme, the dermamyotome and the limb. On the basis of map position and expression pattern, EYA4 is a candidate for oculo-dento-digital (ODD) syndrome, but no EYA4 mutations were found in a panel of ODD patients.
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Abstract
Several cancer genetics centres offer testing for specific BRCA1 and BRCA2 mutations to Ashkenazi Jewish individuals with a family history of breast and ovarian cancers. Testing involves screening for three common mutations found in this population, namely BRCA1 185delAG, 5382insC and BRCA2 6174delT (Struewing et al., Nat Genet 1995: 11: 198-200; Roa et al., Nat Genet 1996: 14: 185-187; Oddoux et al., Nat Genet 1996: 14: 188-190). We have identified a large Ashkenazi Jewish kindred (W9170) with ten cases of breast cancer and four cases of ovarian carcinoma. Initially, mutation analysis for this family identified a BRCA1 185delAG mutation in the proband diagnosed with three separate primary cancers of the breast, ovary and colon. Another individual in this family diagnosed with two primary cancers of the ovary and breast, was identified as having a second mutation, BRCA1 5382insC. Subsequent work found that two sisters (cousins of the proband), both diagnosed with carcinoma of the breast, had a third mutation, BRCA2 6174delT. These three mutations have previously been found to be more common in the Ashkenazi Jewish population (References as above). The identification of all three mutations in one family, raised new implications for the manner in which testing and counselling should be offered. In our opinion, Ashkenazi Jewish individuals in breast-ovarian cancer families should be offered complete testing for the three common Ashkenazi Jewish mutations regardless of previous identification of one of these mutations in the family.
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An elastin gene mutation producing abnormal tropoelastin and abnormal elastic fibres in a patient with autosomal dominant cutis laxa. Hum Mol Genet 1998; 7:1021-8. [PMID: 9580666 DOI: 10.1093/hmg/7.6.1021] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Elastin is the protein responsible for the characteristic elastic properties of many tissues including the skin, lungs and large blood vessels. Loss-of-function mutations in the elastin gene are known to cause the heart defect supravalvular aortic stenosis (SVAS). We and others have identified deletions, nonsense mutations and splice site mutations in SVAS patients that abolish the function of one elastin gene. We have now identified an elastin mutation in a patient with a completely different phenotype, the rare autosomal dominant condition cutis laxa. A frameshift mutation in exon 32 of the elastin gene is predicted to replace 37 amino acids at the C-terminus of elastin by a novel sequence of 62 amino acids. mRNA and immunoprecipitation studies show that the mutant allele is expressed. Electron microscopy of skin sections shows abnormal branching and fragmentation in the amorphous elastin component, and immunocytochemistry shows reduced elastin deposition in the elastic fibres and fewer microfibrils in the dermis. These findings suggest that the mutant tropoelastin protein is synthesized, secreted and incorporated into the elastic matrix, where it alters the architecture of elastic fibres. Interference with cross-linking would reduce elastic recoil in affected tissues and explain the cutis laxa phenotype.
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Abstract
A new live oral cholera vaccine, Peru-15, was studied for safety, immunogenicity, and excretion in 2 groups of healthy volunteers. Twelve inpatient volunteers received freshly harvested vaccine in doses of either 10(7) or 10(9) cfu. Subsequently 50 outpatient volunteers received freeze-dried vaccine in doses of 10(8) or 10(9) cfu or placebo in a three-cell, double-masked, placebo-controlled trial. The strain was well tolerated at all dose levels, and it stimulated high levels of vibriocidal antibodies in most inpatient volunteers and in all outpatient volunteers. Although antitoxin responses were less frequent and of lower magnitude than the vibriocidal responses, antitoxin responses were seen in >60% of the outpatient volunteers. About 60% of the volunteers excreted the vaccine in their feces; however, fecal excretion did not correlate with serologic responses. It is concluded that Peru-15 is a safe and immunogenic oral vaccine for cholera.
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Elastin: genomic structure and point mutations in patients with supravalvular aortic stenosis. Hum Mol Genet 1997; 6:1029-36. [PMID: 9215671 DOI: 10.1093/hmg/6.7.1029] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We describe the complete exon-intron structure of the human elastin (ELN) gene located at chromosome 7q11.23. There are 34 exons occupying approximately 47 kb of genomic DNA. All exons are in-frame, allowing exon skipping without disrupting the reading frame. Microsatellites are located in introns 17 and 18. Deletions of all or large parts of the ELN gene have been previously reported in two patients with supravalvular aortic stenosis (SVAS), and SVAS is also a frequent feature of Williams syndrome, where patients are hemizygous for ELN. We list primer pairs for amplifying each exon, with flanking intron, from genomic DNA to allow detection of point mutations in the ELN gene. We show that some patients with isolated SVAS have point mutations that are predicted to lead to premature chain termination. Knowledge of the genomic structure will allow more extensive mutation screening in genomic DNA of patients with SVAS and other conditions.
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Evaluation of TAP1 polymorphisms with insulin dependent diabetes mellitus in Finnish diabetic patients. The Childhood Diabetes in Finland (DiMe) Study Group. Hum Immunol 1997; 53:159-66. [PMID: 9129974 DOI: 10.1016/s0198-8859(97)00030-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Insulin dependent diabetes mellitus (IDDM) is an autoimmune disease with a strong association between disease and the HLA class II region. Because abnormal antigen processing, in part characterized by altered class I processing, has been identified in patients with IDDM, the TAP (transporter associated with antigen processing) genes located in the HLA class II region make attractive candidate genes for IDDM. Five coding region variants of TAP1 were typed in a cohort of well characterized Finnish patients with diabetes (n = 119) and compared to racially marched control subjects (n = 92). We found that although no single TAP1 polymorphism was associated with IDDM, a genotypic combination of Ile/Val at codon 333 with Asp/Asp at codon 637 was found more frequently in subjects with IDDM (9.4%) compared to controls (1.2%; p = 0.025). This could not be accounted for by an association with any particular haplotype defined by class I or class II serology.
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Abstract
Oculodentodigital syndrome (ODD) is a congenital, autosomal dominant disorder which affects the development of the face, eyes, limbs and dentition. Spastic paraparesis is thought to be an occasional manifestation of the disorder. Type III syndactyly, which occurs as part of ODD, has also been reported to occur as an isolated entity. In the current investigation, a total genome search for the location of the ODD locus was instigated and linkage to polymorphic markers located on chromosome 6q established (pairwise Zmax = 9.37; theta = 0.001). Analysis of a large family with type III syndactyly, but atypical facial features, further suggested that isolated type III syndactyly is also located in this same region of the genome.
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Abstract
MHC Class II genes may contribute to susceptibility to IgA nephropathy (IgAN). We have previously identified a restriction fragment length polymorphism (RFLP) of the DQB1 region that associated with IgAN in British Caucasoids. However, another group, while demonstrating a DQB1 association, was unable to confirm our finding. MHC molecules are heterodimers consisting of an alpha and beta chain, and thus polymorphism of the DQA1 alpha chain may also be important to disease pathogenesis in IgAN. Therefore, we have determined DQA1 alleles and re-examined DQB1 alleles in British Caucasoids with IgAN using an approach that can differentiate between the common DQ alleles; we have also extended our studies to Caucasoid populations from Northern and Southern Europe, thereby addressing the possibility of variation in genetic susceptibility between populations. DNA was prepared from IgAN patients (British, N = 105; Italian, N = 71; Finnish, N = 48) and healthy controls (British, N = 111; Italian, N = 63; Finnish, N = 41). DQA1 alleles were identified by TaqI RFLP and Southern blotting; alleles that could not be fully resolved by Taq Southern blotting were identified by PCR-RFLP. DQB1 alleles were identified by polymerase chain reaction (PCR) based technique (PCR-RFLP). No consistent association of DQ alleles were found between the populations studied. In British patients a decreased frequency of DQB1*0201 was observed (P = 0.008), in Finnish patients a decreased frequency of DQB1*0602 was observed (P = 0.01), and in Italian patients no association between DQ markers and IgAn was found. These data demonstrate population variation in disease association, but no strong or consistent association in the DQ region.
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A gene in the HLA class I region contributes to susceptibility to IDDM in the Finnish population. Childhood Diabetes in Finland (DiMe) Study Group. Diabetologia 1994; 37:937-44. [PMID: 7806025 DOI: 10.1007/bf00400951] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In Finland the haplotype A2, Cw1, B56, DR4, DQ8 is the third most common haplotype in insulin-dependent diabetic (IDDM) patients and has the highest haplotype-specific absolute risk for IDDM. Cw1, B56, DR4, DQ8 haplotypes containing HLA-A alleles other than A2 are infrequent in the population and are not associated with IDDM. Comparison of the A2 and non-A2 haplotypes at the DNA level showed that they were identical at HLA-B, -DR, and -DQ loci. Evidence that class I alleles confer susceptibility to IDDM was obtained from the two HLA-C, -B, -DR and -DQ haplotypes most frequently found in IDDM patients in Finland. A24, A3 and A2 on the Cw3, B62, DR4, DQ8 haplotype, and A28, A2 and A1 on the Cw7, B8, DR3, DQ2 were all found to be associated with IDDM. In Finland these seven haplotypes, including A2, Cw1, B56, DR4, DQ8, account for 33% of diabetic haplotypes and 10.3% of non-diabetic haplotypes (p < 0.00001). The contribution of the class I region to IDDM susceptibility was also apparent in those IDDM patients lacking the disease-predisposing class II alleles. Significantly more non-DR3/non-DR4 IDDM patients (47 of 55) possessed two of the IDDM-associated HLA-A alleles compared to non-DR3/non-DR4 control subjects (40 of 58; p = 0.038). Moreover, IDDM patients confirmed by oligotyping as unable to form a 'diabetes-susceptibility' DQ heterodimer, tended to possess two diabetes-associated HLA-A alleles (12 of 13) compared to control subjects (12 of 20; p = 0.056).
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