The complex polyploid genome architecture of sugarcane

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

A126 ASSESSING THE QUALITY OF REFERRALS AND ADJUDICATION FOR ENDOSCOPIC RESECTION OF LARGE COLORECTAL POLYPS AT A CANADIAN TERTIARY REFERRAL CENTRE

Background

Management of large colorectal polyps is increasingly complex with the expansion of endoscopic techniques, including endoscopic submucosal dissection (ESD), endoscopic mucosal resection (EMR), and endoscopic full thickness resection. Adjudicating lesions in an effort to select the optimal resection method is hugely dependent on the information included within the referral. At our institution, a referral pathway based on photo and/or video documentation was created to facilitate the timely assessment and treatment of large colorectal polyps. To date, little is known about quality of referrals for endoscopic resection of large colorectal polyps.

Purpose

Our study aimed to assess the adjudication process and quality of referrals for endoscopic resection of large colorectal polyps at our advanced endoscopy referral center.

Method

We conducted a single-center prospective study of consecutive colorectal polyps referred for EMR from March 2021 to March 2022. Cases selected upfront for ESD were excluded. Referral information, intraprocedural data and histology was captured. No procedural and histology data were captured if EMR does not occur after adjudication. The outcome was defined as the frequency of adequate referrals. A referral was deemed adequate if it contained: sufficient photo or video documentation, description of any characteristics that increase the difficulty of endoscopic resection, accurate polyp localization/size estimate (with <1 cm discrepancy when compared to real-time endoscopic evaluation), and description of any endoscopic features of advanced dysplasia (AD), including HGD/IMCa, or submucosal invasion (SMI).

Result(s)

During the study period, 213 referrals were received for colorectal polyps and underwent adjudication for EMR: 211 underwent EMR; 2 underwent ESD despite being triaged for EMR. Only 5% (10/213) of referrals were deemed to be adequate. Only 34% (73/213) contained any photo or video documentation and only 13% (28/213) photos/videos were of sufficient quality for adjudication. Difficult location or polyp characteristics, if present, were accurately described in 86.7% of referrals (183/211) of referrals. The accurate polyp location was described 80.6% of the time (170/211). Polyp size was estimated in 50.2% (107/213) of referrals. Amongst referrals with size estimated, the size was accurate in 73.8% of the time (79/107). On histological evaluation, 35.1% (74/211) of polyps had AD or SMI. Amongst polyps with AD or SMI, 48.6% (36/74) had endoscopic appearance suggestive of HGD/IMCa/SMI but only 69.4% (25/36) of these polyps with high-risk endoscopic features were accurately predicted based on the referral information.

Conclusion(s)

Referrals for large colorectal polyps often lack important clinical information. This significantly impairs the ability to adjudicate polyps for triage and resection and may negatively impact patient outcomes. To improve referral adequacy and patient outcomes, we plan to evaluate the impact of polyp adjudication on EMR success.

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None

Disclosure of Interest

None Declared

A228 SAFETY AND EFFICACY OF ENDOSCOPIC RESECTION OF NON-AMPULLARY DUODENAL POLYPS AND RISK OF POLYP RECURRENCE

Background

Non-ampullary duodenal adenomas, which can present sporadically or in the context of a polyposis syndrome, carry a risk of progression to carcinoma in a similar sequence to colorectal adenomas. Complete endoscopic resection is recommended as first line as a less invasive alternative to surgical rsection. Identifying recurrence rates of non-ampullary duodenal polyps after endoscopic resection, and patient and polyp characteristics associated with recurrence is important in determining the best method of resection and guiding endoscopic surveillance.

Purpose

To determine the technical success rate of endoscopic resection of non-ampullary duodenal polyps, complication rates, rate of residual and recurrent polyps, and identify factors associated with polyp recurrence.

Method

All adult patients (≥18 years) that underwent endoscopic resection of non-ampullary duodenal polyps at St. Michael’s Hospital, a Canadian tertiary referral center, from January 2010 to June 2021 were retrospectively identified. Descriptive statistics were calculated for variables of interest and Chi-square, t-test or U-Mann Whitney tests were used to compare variables as appropriate. Bi-variate regression analysis was utilized to determine co-variables associated with recurrence.

Result(s)

A total of 300 patients underwent endoscopic resection of duodenal polyps. Table 1 describes patient demographics, polyp and procedural characteristics and characteristics associated with recurrence. Nearly all cases were technically successful (96%, n=286/299). Clinically significant intraprocedural bleeding occurred in 22% (n=65/300) of patients, and deep mural injury occurred in 3% (n=7/284) of patients. Delayed post-procedural bleeding occurred in 9% of patients (n=26/279). The median time to first surveillance EGD was 4 months. Polyp recurrence occurred in 28% (n=50/180) of patients. Of the patients with polyp recurrence, 82% (n=42/50) were successfully managed endoscopically. On univariate analysis, polyp size (OR 1.03, 95% CI 1.01-1.06), piecemeal resection (OR 1.63, 95% CI 0.17-0.82), intraprocedural bleeding (OR 2.28, 95% CI 1.09-4.74), and high-grade dysplasia (HGD) or intramucosal adenocarcinoma (IMCa) on final histology (OR 3.46, 95% CI 1.64-7.33) were significantly associated with polyp recurrence. On multivariate analysis, only HGD/IMCa on final histology was significant (OR 3.41, 95% CI 1.38-8.47).

Image

Conclusion(s)

Endoscopic resection of duodenal polyps can be safely performed with high technical success, however recurrence is a significant concern. Advanced histology was a significant predictor of polyp recurrence and highlights the importance of accurate pre-resection endoscopic characterization to correctly identify lesions at increased risk that may benefit from alternative resection methods such as ESD or hot rather than cold EMR, and which may require closer follow-up. Future work to develop predictive models of recurrence are needed to better stratify patient risk.

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None

Disclosure of Interest

None Declared

A61 USE OF ADJUNCTIVE REMOVAL TECHNIQUES FOR ENDOSCOPIC MUCOSAL RESECTION OF LARGE NON-PEDUNCULATED COLONIC POLYPS IS PREDICTIVE OF POLYP RECURRENCE

Background

Endoscopic mucosal resection (EMR) allows for safe and effective removal of large non-pedunculated colon polyps. However, prior studies have shown significant recurrence rates between 10–30% after EMR, which have led to recommendations for close endoscopic follow-up and the use of techniques such as snare tip soft coagulation (STSC) to EMR margins to prevent recurrence. Models such as the Size/Morphology/Site/Access score (SMSA) have been developed to aid in identifying polyp complexity and patients at high risk of recurrence. Numerous individual risk factors for recurrence have previously been reported, however the significance of these factors have varied between studies, with limited data from Canadian centres.

Aims

To evaluate predictors of recurrence for large non-pedunculated polyps following EMR.

Methods

Consecutive patients between April 1, 2017 to March 1, 2019 who underwent EMR were retrospectively identified from endoscopy unit administrative records. Patients with non-pedunculated colorectal polyps ≥ 2 cm that were removed by EMR were included if follow-up endoscopy data were available. Polyps found to contain invasive adenocarcinoma on histology and/or were referred for surgical resection were excluded. Patient demographic, pre-procedural, intra-procedural, and post-procedural data to time of first follow-up colonoscopy were extracted. Recurrence was defined as a positive pathology specimen from the EMR scar at follow-up. Adjunctive techniques were defined as the use of any non-snare resection or ablation technique for removal of visible adenoma at the time of the EMR. Chi-square and multivariate regression analyses were conducted for variables of interest.

Results

517 patients underwent large polyp EMR during the study time period with 265 patients satisfying inclusion criteria. Median age of patients was 67 years (IQR 14); 48% were female. STSC was performed to EMR margins in 94% of cases. 30.9% and 69.1% of polyps were SMSA grade 3 and grade 4 respectively. Adjunctive removal techniques were utilized in 31% of patients, 95% of which was hot avulsion. 15% of patients had recurrence on follow-up endoscopy. Higher SMSA grade was associated with the use of adjunctive techniques (20% vs. 37%, p=0.006). The use of adjunctive removal techniques (OR 2.92, p=0.007) and male gender (OR 3.45, p=0.002) were the only factors found to be significantly predictive of recurrence on multivariate analysis.

Conclusions

Male gender and the use of adjunctive removal techniques, particularly hot avulsion, are independently predictive of recurrence after EMR of large complex colorectal polyps. Male patients and those who require hot avulsion may be considered high risk for recurrence and warrant closer follow-up.

Funding Agencies

None

A48 USE OF ENDOSCOPIC ULTRASOUND FINE NEEDLE ASPIRATE AND ENDOSCOPIC ULTRASOUND FINE NEEDLE BIOPSY FOR DETECTION OF GATA6 EXPRESSON IN PANCREATIC DUCTAL ADENOCARINCOMA

Background

GATA6 is a transcription factor that can be used to distinguish between the basal-like and classical subtypes of pancreatic ductal adenocarcinoma (PDAC). The basal-like subtype has been demonstrated to be less responsive to modified FOLFIRINOX chemotherapy and thus can be used to predict response to specific chemotherapies. To date, GATA6 expression has only been evaluated in surgically resected PDAC specimens. Less than 15% of patients with PDAC are eligible for surgery. Endoscopic ultrasound guided fine-needle aspirate (EUS-FNA) and biopsy (EUS-FNB) can potentially help assess GATA6 expression in PDAC and in turn, help guide personalized treatment selection in all cases of PDAC.

Aims

The primary objective of this study was to explore the yield of EUS-FNA and EUS-FNB for the detection of GATA6 among patients with PDAC. The study also aimed to explore the impact of lesion location on sample adequacy and type of fixative on validity of GATA6 staining.

Methods

This study was conducted from November 2017 to October 2019. Consecutive patients with a diagnosis of PDAC confirmed by biopsy were included. Patients underwent either EUS-FNB or EUS-FNA to obtain tissues samples. Samples were fixed in either neutral buffered formalin (NBF) or a methanol based buffered solution (Cytolyt) and evaluated by a specialized cytopathology team. Fisher’s exact test was used and a p-value ≤0.05 was considered to indicate statistical significance.

Results

Forty-four patients were included in the study. Twenty-three (52%) patients were male and the median age of patients was 67.5 years. Twenty-five lesions were located in the head and neck of the pancreas, 14 were located in the body, and 4 were located in the tail. One patient was found to have a local recurrence of PDAC at the surgical bed of a previous Whipple procedure.

Eighteen lesions were sampled by EUS-FNA and 26 were sampled using EUS-FNB. Thirty-eight (86%) samples were adequate for assessment of GATA6. Sampling technique (p=0.68) and fixative type (p=1.00) did not appear to affect sample adequacy. Compared to pancreatic body or tail specimens, samples obtained from the head or neck of the pancreas were more likely to be inadequate for analysis (p=0.03).

Conclusions

EUS-FNA and EUS-FNB samples are efficacious methods of assessing GATA6 expression in PDAC. This is the first predictor of treatment response that has been demonstrated to be obtained without surgical resection. Neither EUS needle type or alcohol fixation before cell block preparation appear to impact GATA6 detection. Lesions in the pancreatic head or neck appear to be associated with higher rates of sample inadequacy. Larger, prospective studies are required to confirm our findings.

Funding Agencies

None

A82 A SURVEY OF TRAINING PATHWAYS AND PRACTICE TRENDS OF ENDOSCOPIC SUBMUCOSAL DISSECTION IN CANADA

Background

Endoscopic submucosal dissection (ESD) has become the established standard for endoscopic removal of large gastrointestinal (GI) lesions and early GI malignancies, with improved outcomes compared to traditional endoscopic techniques and offers an alternative to surgery. However, ESD is technically challenging and requires significant healthcare infrastructure. As such, its adoption in Canada was slow relative to Asia and Europe. Thus far, the practice of ESD has been limited to a small number of tertiary centers. Currently, the availability and practice of ESD across Canada remains unclear.

Aims

To provide a descriptive overview of the training pathways and practice trends of endoscopists performing ESD in Canada.

Methods

ESD practitioners across Canada were identified from internal networks and by contacting respective endoscopy units. All endoscopists currently accepting ESD referrals were invited to participate in a cross-sectional survey that was distributed via SurveyMonkey.

Results

27 ESD practitioners were identified; current survey response rate was 44% although is expected to increase. Median years of independent ESD practice was 5 (IQR 2.75). All practitioners underwent international ESD training of some type. 92% attended short-term training courses. 50% pursued international ESD fellowship training. 92% received training on animal models. 58% and 33% performed hands-on human upper and lower GI ESD respectively prior to independent practice. In practice, 67% of practitioners noted an increase in number of ESD procedures performed per year from 2015 to 2019. 67% rated the awareness of appropriate ESD indications by referring physicians to be “not so aware” or lower. 75% of practitioners report a patient wait time for ESD of 1–3 months. 67% and 75% rated the difficulty of securing endoscopy time and anesthesia support for ESD respectively to be “difficult” or “very difficult”. 75% were “dissatisfied” or “very dissatisfied” with their institution’s healthcare infrastructure to support ESD. 25% perceived their institution as supportive in expanding the practice of ESD.

Conclusions

A number of challenges exist for the adoption of ESD in Canada. Training pathways are highly variable, with no set standards and most practitioners pursue international training. In practice, the majority of practitioners express dissatisfaction with their access to necessary infrastructure for performing ESD and feel poorly supported by their centers in expanding its practice. As ESD is becoming the accepted standard in allowing for the minimally invasive treatment of indicated GI lesions; greater collaboration between practitioners, institutions, and healthcare systems is crucial to standardize ESD training and to ensure improved patient access.

Funding Agencies

None

A272 THE CANADIAN DIRECT OBSERVATION OF PROCEDURAL SKILLS (CANDOPS) TOOL FOR ENDOSCOPIC RETROGRADE CHOLANGIOPANCREATOGRAPHY: A MULTI-CENTRE PROSPECTIVE STUDY

Background

Previous studies have demonstrated that many graduating trainees may not have all of the skills needed to independently practice endoscopic retrograde cholangiopancreatography (ERCP) safely and effectively. As a part of competency-based learning curriculum development, it is essential to provide formative feedback to trainees and ensure they acquire the knowledge and skills for independent practice.

Aims

To assess the performance of advanced endoscopy trainees across Canada using the Canadian Direct Observation of Procedural Skills (CanDOPS) ERCP assessment tool. Procedural items evaluated include both technical (cannulation, sphincterotomy, stone extraction, tissue sampling, and stent placement) and non-technical (leadership, communication and teamwork, judgment and decision making) skills.

Methods

We conducted a prospective national multi-centre prospective study. Advanced endoscopy trainees with at least two years of gastroenterology training or five years of general surgery in North America and minimal experience performing ERCPs (less than 100 ERCP procedures) were invited to participate. The CanDOPS tool was used to measure every fifth ERCP performed by trainees over a 12-month fellowship training period. ERCPs were evaluated by experienced staff endoscopists at each study site under standard clinical protocol. Cumulative sum (CUSUM) analyses were used to generate learning curves.

Results

The data from five Canadian sites and 11 trainees participated in the study. A total of 261ERCP evaluations were completed. Median number of evaluations by site and trainee was 49 (IQR 31–76) and 15 (IQR 11–45). Median number of cases trainees performed prior to their ERCP training was 50 (IQR 25–400). There was a significant improvement in almost all scores over time, including selective cannulation, sphincterotomy, biliary stenting and all non-technical skills (P&lt;0.01). CUSUM analyses using acceptable and unacceptable failure rates of 20% and 50% demonstrated trainees achieved competency for most measures in their final month of their training. Competency in tissue sampling was not achieved within a one-year training period.

Conclusions

This is the first ERCP performance evaluation tool that examines multiple technical and non-technical aspects of the procedure. Although trainee ERCP skills do improve during their training period, there exists a notable variability in time to competency for the different skills measured using the CanDOPS tool. Large prospective research is required to determine if competency is achieved using more stringent definitions of ERCP competency and to determine factors associated with reaching competency.

Funding Agencies

None

A279 EUS-GUIDED BILIARY DRAINAGE IN MALIGNANT DISTAL BILIARY OBSTRUCTION: AN INTERNATIONAL SURVEY TO IDENTIFY BARRIERS OF TECHNOLOGY IMPLEMENTATION

Background

Endoscopic ultrasound-guided biliary drainage (EUS-BD) is a promising alternative to endoscopic retrograde cholangiopancreatography (ERCP) in malignant distal biliary obstruction (MDBO). Recent small randomized controlled trials comparing EUS-BD with ERCP suggest that EUS-BD achieves a similar technical success rate and safety profile while potentially being associated with lower rates of stent dysfunction However, its application in clinical practice has been impeded by various undefined barriers.

Aims

To evaluate the current practice of EUS-BD and the determinants for its clinical implementation in MDBO.

Methods

An online survey was generated using Google Forms. Five endoscopy societies have distributed the survey as of October 10th, 2019. Survey questions measured participant characteristics, EUS-BD in different clinical scenarios, and potential barriers to implementation. Descriptive statistics were calculated using frequencies, chi-square statistics were used for inferential analysis, and a standard step-wise multivariable analysis was performed to identify independent variables for and against the use of EUS-BD.

Results

To date, 102 physicians have participated in the survey (response rate 7.97%). The majority of participants are from North America (39.2%), Asia (31.4%), and Europe (19.6%). Most participants are gastroenterologists with formal therapeutic endoscopy training (66.7%), though only 28.4% have received EUS-BD training. In unresectable cancer, 85.1% of respondents favoured EUS-BD over percutaneous biliary drainage following ERCP failure (p&lt;0.0001), while in borderline resectable disease, 72.3% preferred EUS-BD. On multivariable analysis, male gender, formal training in EUS-BD, and unresectable cancer were independent variables for the use of EUS-BD. Conversely, independent discouraging factors for EUS-BD included fear of adverse events, limited high-quality data, lack of local expertise, and inadequate access to EUS technology.

Conclusions

In this international survey, it appears that EUS-BD is gaining traction, especially in the setting of unresectable disease following ERCP failure. However, barriers to implementation include the lack of high-quality data, fear for adverse events, limited experts in the field, and inadequate access to EUS technology. This suggest the need for high-quality clinical trials, increased endoscopist training in this field, and further technology development in EUS-BD in order to increase its uptake in clinical practice.

Funding Agencies

None

Author Correction: Osmotic modulation of chromatin impacts on efficiency and kinetics of cell fate modulation

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Osmotic modulation of chromatin impacts on efficiency and kinetics of cell fate modulation

Chromatin structure is a major regulator of transcription and gene expression. Herein we explore the use of osmotic modulation to modify the chromatin structure and reprogram gene expression. In this study we use the extracellular osmotic pressure as a chromatin structure and transcriptional modulator. Hyposmotic modulation promotes chromatin loosening and induces changes in RNA polymerase II (Pol II) activity. The chromatin decondensation opens space for higher amounts of DNA engaged RNA Pol II. Hyposmotic modulation constitutes an alternative route to manipulate cell fate decisions. This technology was tested in model protocols of induced pluripotency and transdifferentiation in cells growing in suspension and adherent to substrates, CD34⁺ umbilical-cord-blood (UCB), fibroblasts and B-cells. The efficiency and kinetics of these cell fate modulation processes were improved by transient hyposmotic modulation of the cell environment.

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees

Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.

Search for gravitational waves associated with γ-ray bursts detected by the interplanetary network

We present the results of a search for gravitational waves associated with 223 γ-ray bursts (GRBs) detected by the InterPlanetary Network (IPN) in 2005-2010 during LIGO's fifth and sixth science runs and Virgo's first, second, and third science runs. The IPN satellites provide accurate times of the bursts and sky localizations that vary significantly from degree scale to hundreds of square degrees. We search for both a well-modeled binary coalescence signal, the favored progenitor model for short GRBs, and for generic, unmodeled gravitational wave bursts. Both searches use the event time and sky localization to improve the gravitational wave search sensitivity as compared to corresponding all-time, all-sky searches. We find no evidence of a gravitational wave signal associated with any of the IPN GRBs in the sample, nor do we find evidence for a population of weak gravitational wave signals associated with the GRBs. For all IPN-detected GRBs, for which a sufficient duration of quality gravitational wave data are available, we place lower bounds on the distance to the source in accordance with an optimistic assumption of gravitational wave emission energy of 10(-2)M⊙c(2) at 150 Hz, and find a median of 13 Mpc. For the 27 short-hard GRBs we place 90% confidence exclusion distances to two source models: a binary neutron star coalescence, with a median distance of 12 Mpc, or the coalescence of a neutron star and black hole, with a median distance of 22 Mpc. Finally, we combine this search with previously published results to provide a population statement for GRB searches in first-generation LIGO and Virgo gravitational wave detectors and a resulting examination of prospects for the advanced gravitational wave detectors.

Search for gravitational waves associated with γ-ray bursts detected by the interplanetary network

We present the results of a search for gravitational waves associated with 223 γ-ray bursts (GRBs) detected by the InterPlanetary Network (IPN) in 2005-2010 during LIGO's fifth and sixth science runs and Virgo's first, second, and third science runs. The IPN satellites provide accurate times of the bursts and sky localizations that vary significantly from degree scale to hundreds of square degrees. We search for both a well-modeled binary coalescence signal, the favored progenitor model for short GRBs, and for generic, unmodeled gravitational wave bursts. Both searches use the event time and sky localization to improve the gravitational wave search sensitivity as compared to corresponding all-time, all-sky searches. We find no evidence of a gravitational wave signal associated with any of the IPN GRBs in the sample, nor do we find evidence for a population of weak gravitational wave signals associated with the GRBs. For all IPN-detected GRBs, for which a sufficient duration of quality gravitational wave data are available, we place lower bounds on the distance to the source in accordance with an optimistic assumption of gravitational wave emission energy of 10(-2)M⊙c(2) at 150 Hz, and find a median of 13 Mpc. For the 27 short-hard GRBs we place 90% confidence exclusion distances to two source models: a binary neutron star coalescence, with a median distance of 12 Mpc, or the coalescence of a neutron star and black hole, with a median distance of 22 Mpc. Finally, we combine this search with previously published results to provide a population statement for GRB searches in first-generation LIGO and Virgo gravitational wave detectors and a resulting examination of prospects for the advanced gravitational wave detectors.

Constraints on cosmic strings from the LIGO-Virgo gravitational-wave detectors

Cosmic strings can give rise to a large variety of interesting astrophysical phenomena. Among them, powerful bursts of gravitational waves (GWs) produced by cusps are a promising observational signature. In this Letter we present a search for GWs from cosmic string cusps in data collected by the LIGO and Virgo gravitational wave detectors between 2005 and 2010, with over 625 days of live time. We find no evidence of GW signals from cosmic strings. From this result, we derive new constraints on cosmic string parameters, which complement and improve existing limits from previous searches for a stochastic background of GWs from cosmic microwave background measurements and pulsar timing data. In particular, if the size of loops is given by the gravitational backreaction scale, we place upper limits on the string tension Gμ below 10(-8) in some regions of the cosmic string parameter space.

Severe ARDS induced by fusobacterial infections: a rare clinical presentation of Lemierre syndrome

Acute respiratory distress syndrome (ARDS) poses a major challenge in intensive care settings. The main underlying causes of ARDS are trauma, pancreatitis, and pulmonary manifestation of systemic inflammatory response syndrome/sepsis.Lemierre syndrome represents a nearly forgotten entity arising from oropharyngeal infections with Fusobacterial species, and it is of renewed and increasing interest because of evolving antibiotic resistances.We report two cases of young female patients afflicted by Lemierre syndrome with additional severe ARDS and present an overview of the current literature.

Length of Barrett's segment predicts success of extensive endomucosal resection for eradication of Barrett's esophagus with early neoplasia

BACKGROUND

Although the efficacy and safety of extensive endomucosal resection (EMR) in eradicating Barrett's esophagus (BE) harbouring early neoplasia have been established, factors predicting efficacy remains unclear.

AIM

To determine the complete eradication rate of Barrett's esophagus with high-grade intraepithelial neoplasia (HGIN) or intramucosal carcinoma (IMC), safety, and factors predicting complete eradication by EMR.

METHODS

Patients with histological confirmation of Barrett's HGIN/IMC were prospectively identified. EMR was performed using Duette multiband ligator or cap technique by a single operator (NEM).

RESULTS

99 patients (81 males) with median age 67 years [interquartile range (IQR) 60-77 years] and median Barrett's length 4 cm (IQR 2-6 cm) were included. Of 628 index EMRs [mean 6.3, median 5 (IQR 3-8)], 23% showed IMC, 58.5% showed HGIN, and 16% showed low-grade dysplasia only. A median of 8 EMR resections per patient (IQR 6-16, 1,064 resections in 89 patients) resulted in complete eradication of BE harboring neoplasia in 49.4% and eradication of HGIN/IMC in 81% (BE <5 cm subgroup: 65% complete eradication and 91% HGIN eradication) at median follow-up of 18 months (range 6-27 months). On univariate analysis, focal dysplasia (P = 0.003) and Barrett's length <5 cm (P = 0.001) were predictors of complete BE eradication. Barrett's length <5 cm was the only significant predictor [odds ratio (OR) 3.4, standard error (SE) 0.11, P = 0.0006] on multiple logistic regression analysis. Strictures developed in 27% and major bleeding in 2% with no procedure-related perforations or mortality.

CONCLUSIONS

Extensive EMR for removal of BE with early neoplasia is safe. Outcomes for complete BE eradication are modest at 49.4% and eradication of high-grade dysplasia at 81%. Barrett's length <5 cm is the only significant predictor of complete response.

Growth of GaN on Lithium Gallate Substrates for Development of a GaN Thin Compliant Substrate

The GaN on LGO system is the near perfect template (due to extremely high etch selectivity) for developing a viable thin film/compliant GaN substrate. Herein, we report on our efforts to grow GaN on LGO, including improvement of the microscopic surface morphology using pre-growthpretreatments. We also report on the first transferred thin film GaN substrate grown on LGO, transferred off of LGO, and mounted on GaAs. With this approach, (InAl)GaN alloys can be grown on thin GaN films, implementing a truly “compliant” substrate for the nitride alloy system. In addition, the flexibility of bonding to low cost Si, metal or standard ceramic IC packages is an attractive alternative to SiC and HVPE GaN substrates for optimizing cost verses thermal conductivity concerns. We have demonstratedhigh quality growth of GaN on LGO. X-Ray rocking curves of 145 arc-seconds are obtained with only a 0.28 μm thick film. We present data on the out of plane crystalline quality of GaN/LGO material. Likewise, we show 2 orders of magnitude improvement in residual doping concentration and factors of 4 improvement in electron mobility as compared to the only previously reported electrical data. We show substantial vendor to vendor and intra-vendor LGO material quality variations. We have also quantified the desorption of Ga and Li from the surface of LGO at typical growth temperatures using in situ desorption mass spectroscopy and XPS.

Living Kidney Donation: Anemia and Inflammation in the Early Postoperative Period

Studies on living donor kidney transplantation primarily address the recipients; few publications focus on kidney donors. The aim of the present study was to detect changes in and compensations of defined parameters of anemia and inflammation in the immediate postnephrectomy period. We included six living kidney donors who underwent an open anterior-extraperitoneal nephrectomy. We excluded donors with complications, such as significant blood loss or infection. Blood samples were taken before nephrectomy as well as on postoperative days 1, 3, 5, and 7, and at discharge for measurements of hemoglobin (Hb), serum erythropoietin (Epo), reticulocytes (Reti), pentraxin 3 (PTX3), and C-reactive protein (CRP). There was a significant decrease in Hb (>3 g/dL), reaching a maximum on day 3 followed by a significant threefold increase in Epo levels on day 5 and a nonsignificant elevation of Reti count. CRP increased approximately 80-fold on day 3. PTX3 showed a similar course, peaking on day 3 with an approximate 70-fold increase. After living donor nephrectomy, there was an unexpectedly pronounced inflammatory reaction in the absence of any signs of bacterial infection simultaneous with a significant decrease in Hb. These parameters improved during the hospital stay, in some cases they achieved the prenephrectomy level at discharge. These data may assist in interpreting laboratory results after nephrectomy among living kidney donors.

What theAspergillusgenomes have told us

The sequencing and annotation of the genomes of the first strains of Aspergillus nidulans, Aspergillus oryzae, and Aspergillus fumigatus will be seen in retrospect as a transformational event in Aspergillus biology. With this event the entire genetic composition of A. nidulans, the sexual experimental model organism of the genus Aspergillus, A. oryzae, the food biotechnology organism which is the product of centuries of cultivation, and A. fumigatus, the most common causative agent of invasive aspergillosis is now revealed to the extent that we are at present able to understand. Each genome exhibits a large set of genes common to the three as well as a much smaller set of genes unique to each. Moreover, these sequences serve as resources providing the major tool to expanding our understanding of the biology of each. Transcription profiling of A. fumigatus at high temperatures and comparative genomic hybridization between A. fumigatus and a closely related Aspergillus species provides microarray based examples of the beginning of functional analysis of the genomes of these organisms going forward from the genome sequence.

Effect of ATG prophylaxis in sensitized and non-sensitized kidney graft recipients

In our effort to find an optimum immunosuppressive protocol for kidney transplantation we introduced two forms of ATG prophylaxis: 1. high-dose single-bolus prophylaxis (9 mg/kg) in non-sensitized patients (PRA < 5%); and 2. low-dose 8-day prophylaxis (1.5-3.0 mg/kg) in sensitized patients (PRA > 5%). A total of 204 kidney graft recipients were included in this study and treated with a triple-drug therapy (TDT). In comparison with TDT-treated controls, in sensitized patients the 8-day ATG prophylaxis resulted in a reduced rate of rejection episodes (25.5% vs 47%), an improved 1-year graft survival (82% vs 71%) and patient survival (94% vs 90%). In non-sensitized patients the high-dose single-bolus ATG prophylaxis induced a T-cell lymphopenia lasting 4 to 5 days and, in comparison with the corresponding controls, resulted in a shortened hospital stay (31.2 days vs 36.7 days), a reduced rate of rejection episodes (25.5% vs 53%), an improved 1-year graft survival (92% vs 86%) and patient survival (100% vs 94%).

A system for studying genetic changes in Candida albicans during infection

Candida albicans is a diploid yeast with a dimorphic life history. It exists commensally in many healthy humans but becomes a potent pathogen in immunocompromised hosts. The underlying genetic mechanisms by which C. albicans switches from a commensal to a pathogenic form in the host are not well understood. To study the evolution of virulence in mammalian hosts, we used GAL1 as selectable marker system that allows for both positive and negative selection in selective media. We show that the deletion of one or both copies of GAL1 in the C. albicans genome does not change virulence in a systemic mouse model. We obtained estimates for the frequency of mitotic recombination at the GAL1 locus during systemic infection. Our observations suggest that genetic changes such as mitotic recombination and gene conversion occur at a high enough frequency to be important in the transition of C. albicans from a commensal to a pathogenic organism.

Pancreatitis in HIV infection: predictors of severity

OBJECTIVES

Acute pancreatitis occurs at greater frequency in HIV-infected patients than in the general population. We set out to determine the frequency of severe acute pancreatitis in HIV-positive patients and to study the accuracy of The Acute Physiology and Chronic Health Evaluation (APACHE II), Ranson, and Glasgow scales for prediction of clinical disease severity.

METHODS

A total of 73 HIV-infected patients with acute pancreatitis were identified retrospectively. Demographic and clinical parameters as well as clinical outcomes were established. Sensitivities and specificities of the three scales mentioned above were calculated and compared.

RESULTS

Of the patients, 63 (83.6%) had AIDS. The majority of cases were medication-induced (46%) or idiopathic (26%). The incidence seemed to be declining in the late 1990s. Eleven patients (15%) had a severe course as defined by death, admission to the intensive care unit, or local complications requiring surgery. Eighteen case (24.6%) were considered severe as defined by the criteria established at the International Symposium on Acute Pancreatitis in Atlanta in 1992. APACHE II criteria best predicted outcome with an overall accuracy of 75% (Glasgow 69%, Ranson 48%). Maximal accuracy was achieved with cut-offs of 14 for APACHE II and 4 for the Glasgow and Ranson criteria.

CONCLUSIONS

HIV-infected patients have a clinical outcome similar to that of the general population. Clinical predictive scales are applicable and useful in this population.

Oral 5-aminosalicylic acid for maintenance of remission in ulcerative colitis

BACKGROUND

The newer 5-ASA preparations were intended to avoid the adverse effects of SASP while maintaining its therapeutic benefits. The efficacy and safety of 5-ASA preparations have been evaluated in numerous clinical trials that have often lacked sufficient statistical power to arrive at definitive conclusions. Previously, it was found that newer 5-ASA drugs were more effective than placebo but no more effective than SASP in inducing remission in ulcerative colitis. This updated review includes more recent studies and evaluates the effectiveness, dose-responsiveness, and safety of 5-ASA preparations in terms of more precise outcome measures.

OBJECTIVES

To assess the efficacy, dose-responsiveness and safety of the newer release formulations of 5-aminosalicylic acid (5-ASA) compared to placebo or sulfasalazine (SASP) in the maintenance of remission in ulcerative colitis.

SEARCH STRATEGY

A computer-assisted literature search for relevant studies (1981-2002) was performed using MEDLINE, BIOS, the Cochrane Controlled Trials Register, the Cochrane IBD Group Specialized Trials Register, and the Science Citation Index, followed by a manual search of reference lists from previously retrieved articles, review articles, symposia proceedings, and abstracts from major gastrointestinal conferences.

SELECTION CRITERIA

Studies were accepted for analysis if they were prospective, randomized, double-blinded, and placebo- or SASP-controlled clinical trials of parallel design with treatment duration of at least six months.

DATA COLLECTION AND ANALYSIS

Based on an intention to treat principle, the primary outcome was the failure to maintain clinical or endoscopic remission. Secondary outcomes were the number of patients experiencing adverse events, the number of patients withdrawn due to adverse events, and exclusions or withdrawals after entry into the study (not due to relapse). All data were analyzed using the Peto odds ratio and corresponding 95% confidence intervals (CI).

MAIN RESULTS

The Peto odds ratio for the failure to maintain clinical or endoscopic remission (withdrawals and relapses) for 5-ASA versus placebo was 0.47 (95% CI, 0.36 to 0.62) with an NNT of 6. These values were also calculated for the trials in which SASP and 5-ASA were compared, revealing an odds ratio of 1.29 (95% CI, 1.05 to 1.57), with a negative NNT value (-19), suggesting a higher degree of therapeutic effectiveness for SASP. SASP and 5-ASA had similar adverse event profiles, with odds ratios of 1.16(0.62 to 2.16), and 1.31(0.86 to 1.99), respectively. The NNH values were determined to be 171 and 78 respectively.

REVIEWER'S CONCLUSIONS

The newer 5-ASA preparations were superior to placebo in maintenance therapy. However, the newer preparations had a statistically significant therapeutic inferiority relative to SASP. This review updates the existing review of oral 5-aminosalicylic acid for maintenance of remission in ulcerative colitis which was published in the Cochrane Library (Issue 3, 2002).

Evaluation of two enzyme immunoassays for detection of human rotaviruses in fecal specimens

The two assays evaluated in this study (the Ridascreen rotavirus and the Pathfinder rotavirus) exhibited comparable sensitivities (100%) but highly divergent positive predictive values (93.74 and 57.7%, respectively) when compared on 393 specimens. This difference should be considered when using these tests on collectives with an unknown or low prevalence.

Pretransplant serum IgA concentration and IgA-anti-Fab autoantibody activity as prognostic indicators of kidney graft survival

IgA concentration and IgA-anti-Fab autoantibody activity were tested in pretransplant sera of 308 kidney graft recipients. Recipients with a serum IgA concentration of 2 g/l or greater had a 1-year graft survival rate of 83%, compared with a 68% rate in recipients with serum IgA of less than 2 g/l (P < 0.005). Serum IgA concentration and IgA-anti-Fab autoantibody activity were significantly associated (r = 0.38, P < 0.0001). Recipients with a high pretransplant IgA-anti-Fab activity had a significantly better graft survival rate (81%) than patients with low pretransplant IgA-anti-Fab (67%, P < 0.025). When IgA-anti-Fab and serum IgA were considered together, 137 recipients with high IgA-anti-Fab and high serum IgA had a 86% 1-year graft survival rate, which was significantly better than the 63% survival rate in patients with low IgA-anti-Fab and low serum IgA (P < 0.0005). The pretransplant serum IgA level and IgA-anti-Fab autoantibody activity were excellent predictors of kidney graft outcome.

Effects of PUVA therapy on kidney allografts: results of a randomized prospective double-blind study

After successful experimental organ transplant studies on the efficacy of PUVA therapy combining donor pretreatment with the photosensitizer 8-methoxypsoralen (P) and the ex vivo irradiation of organs with long-wave ultraviolet light (UVA) prior to transplantation, we started in 1989 the first randomized, prospective, double-blind study to clarify the efficacy of PUVA therapy in human kidney transplantation. This study included 50 kidney donors, 25 of whom were PUVA-treated. A total of 75 kidneys were transplanted in Berlin, Halle and Rostock. The complete data of these 75 recipients were available for the final evaluation. The PUVA group (n = 36) and the non-PUVA group (n = 39) were not statistically significantly different as to donor and recipient data. Regarding the results, no differences were seen in initial hospitalization time, early graft function, rejection rate, number and time of rejection episodes. After a follow-up of 24 months, both graft survival (PUVA vs. non-PUVA: 75% vs. 71.8%) and patient survival (97.2% vs. 97.4%, respectively) were comparably high. PUVA therapy did not influence the development of vascular rejection. Interestingly, the rate of late graft loss after the 6th posttransplant month was lower, but not statistically significantly so, in the PUVA than in the non-PUVA-group (2 vs. 6 graft losses). Thus, PUVA-pretreated kidneys may be associated with a reduced development of chronic rejection.

Cystadenoma of the liver without mesenchymal stroma in a female following hormonal therapy for acne

BACKGROUND

Liver cystadenomas are relatively rare tumours that can be difficult to diagnose; treatment entails complete surgical extirpation either by either anatomical resection or enucleation.

CASE OUTLINE

A 19-year-old woman presented with acute onset of abdominal pain and was found to have a multilocular giant liver cyst.The cyst was percutaneously drained; CEA and CA 19-9 tumour markers were elevated in this cyst fluid: CEA 96 microg/L, CAI9-9 37 550 kU/L. The cyst was completely enucleated and has not recurred. Pathological examination confirmed a cystadenoma without mesenchymal stroma, and tumour oestrogen and progesterone receptors were negative.

DISCUSSION

This is the fourth report of a liver cystadenoma without mesenchymal stroma in a female and the first to document elevated cyst fluid tumour markers. This case also illustrates the possible relationship between hormonal therapy and tumour growth.

Itraconazole-amphotericin B antagonism in Aspergillus fumigatus: an E-test-based strategy

We examined an E-test-based strategy for testing the combination of itraconazole and amphotericin B, the latter given either sequentially or concomitantly, in isolates of Aspergillus fumigatus. An antagonistic interaction between the two drugs was noted, especially with the sequential administration of amphotericin B. This in vitro antagonism was reversible.

Conidial germination in Aspergillus nidulans requires RAS signaling and protein synthesis

The dormant spores of Aspergillus nidulans become competent for growth and nuclear division in a process called conidial germination. To analyze the molecular details of conidial germination, we developed a genetic screen in which we identified spore germination-deficient mutants that are blocked in this process at the restrictive temperature. These mutants defined eight genes, of which we identified five. Four of the five were directly involved in translation and protein folding, and the fifth showed a high degree of homology to a malonyl CoA synthetase. These results suggest that out of a wide array of processes occurring during conidial germination, translation is essential if germination is to proceed. We also show that conidia containing a mutant-activated form of rasA, the ras homologue in A. nidulans, germinate in the absence of an inducing carbon source, suggesting an important role for rasA signaling in conidial germination. Together these data suggest a model by which a carbon source activates a ras-dependent sensory mechanism, inducing translation and leading to conidial germination. This study shows that conidial germination in A. nidulans requires protein synthesis and that the initiation of translation is linked, through an as yet to be determined signaling cascade that includes rasA, to a carbon-source-sensing apparatus.

Azathioprine or 6-mercaptopurine for inducing remission of Crohn's disease

OBJECTIVES

To determine the effectiveness of azathioprine and 6-mercaptopurine in inducing remission of active Crohn's disease.

SEARCH STRATEGY

Studies were selected using the MEDLINE data base (1966 - December 1997), abstracts from major gastrointestinal meetings and references from published articles and reviews. The Cochrane Controlled Trials Register and the Inflammatory Bowel Disease Review Group Trials Register was also searched.

SELECTION CRITERIA

Eight randomized placebo controlled trials of azathioprine and 6-mercaptopurine therapy in adult patients were identified: five dealt with active disease and three had multiple therapeutic arms.

DATA COLLECTION AND ANALYSIS

Data were extracted by three independent observers based on the intention to treat principle. Each study was given a quality score based on predetermined criteria. Extracted data were converted to 2X2 tables (response versus no response and antimetabolite versus placebo) and then synthesized into a summary test statistic using the pooled odds ratio and 95% confidence intervals as described by Cochran and Mantel and Haenszel ('Odds Ratio' in MetaView).

MAIN RESULTS

The odds ratio of a response to azathioprine or 6-mercaptopurine therapy compared with placebo in active Crohn's disease was 2.36 (95% CI 1.57-3.53). This corresponded to a number needed to treat of about 5 to observe an effect of therapy in one patient. When the two trials using 6-mercaptopurine in active disease were excluded from the analysis, the odds ratio of response was 2.04 (CI 1.24 - 3.35). Treatment >/= 17 weeks increased the odds ratio of a response to 2.51 (CI 1.63-3. 88). A steroid sparing effect was seen with an odds ratio of 3.86 (CI 2.14 - 6.96), corresponding to a number needed to treat of about 3 to observe steroid sparing in one patient. Adverse events requiring withdrawal from a trial, principally allergy, leukopenia, pancreatitis, and nausea were increased on therapy with an odds ratio of 3.01 (CI 1.30 - 6.96). The number needed to treat to observe one adverse event in one patient treated with azathioprine or 6-mercaptopurine was 14.

REVIEWER'S CONCLUSIONS

Azathioprine and 6-mercaptopurine are effective therapy for inducing remission in active Crohn's disease. The odds ratio of response increases after >/= 17 weeks of therapy, suggesting that there is a minimum length of time for a trial of azathioprine or 6-mercaptopurine therapy. Adverse events were more common among patients on therapy.

Evolution of poliovirus type I during 5.5 years of prolonged enteral replication in an immunodeficient patient

Poliovirus type 1 was isolated from an immunodeficient patient 4 days after onset of paresis (IS1) and after 5.5 years of prolonged enteral virus replication (IS2). Antigenic characterization revealed that IS1 was Sabin 1-like, whereas IS2 reacted like poliovirus 1 Mahoney. Complete genomic sequencing demonstrated the phylogenetic relationship (94.9% identity) of IS1 and IS2, which differed from the most closely related Sabin 1 by 5.4 and 8.3%, respectively. Both isolates had revertant-like mutations at nucleotides 480 and 6203. Deduced amino acid sequences indicated significant changes between IS1 and IS2 at the neutralizing antigenic site 1. Prolonged enteral replication, evolution, and shedding of poliovirus by immunodeficient patients should be considered in the poliovirus eradication strategy.

CAREN--Computer Assisted Rehabilitation Environment

The CAREN project concerns the development of a virtual reality environment in which the agility of healthy subjects and patients can be tested in a variety of reproducible conditions. CAREN is made by customizing hardware and developing software to enable measurements of motion of a subject in detail as a response to a perturbation from the computer driven motion platform. After feeding the data in a human body model simulation, joint moments of force and muscle activation can be calculated. From the time patterns of these responses, inferences can be made concerning the motor programs the subjects launch. Any primary problem in a motor program, resulting in functional failure or inadequacy, can be identified down to the joint and muscle group. Secondary adaptations of patients to a limitation in the periphery (such as lack of muscle force) can be separated from the primary ones. Inadequacy of complete motor programs in children with movement disorders can be classified, recorded and related to progress that may occur. Especially the understanding of compensation strategies in patients may lead to a better therapeutic attitude. CAREN offers not only a test environment with means of almost unlimited exploratory behaviors for patients, but constitutes also a strong tool for motor control research.