Insights into mammalian TE diversity through the curation of 248 genome assemblies

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

Horizontal transfer of transposable elements is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of transposable elements at what appears to be a high rate compared to other mammals. We investigated the occurrence of horizontally transferred DNA transposons involving bats. We found over 200 putative horizontally transferred elements within bats; sixteen transposons were shared across distantly related mammalian clades and two other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.

Methodologies for the De novo Discovery of Transposable Element Families

The discovery and characterization of transposable element (TE) families are crucial tasks in the process of genome annotation. Careful curation of TE libraries for each organism is necessary as each has been exposed to a unique and often complex set of TE families. De novo methods have been developed; however, a fully automated and accurate approach to the development of complete libraries remains elusive. In this review, we cover established methods and recent developments in de novo TE analysis. We also present various methodologies used to assess these tools and discuss opportunities for further advancement of the field.

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.

The transposable element-rich genome of the cereal pest Sitophilus oryzae

BACKGROUND

The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions.

RESULTS

We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis.

CONCLUSIONS

Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

P14.41 Cost-effectiveness of FET PET for early treatment response assessment in glioma patients following adjuvant temozolomide chemotherapy

BACKGROUND

In light of increasing healthcare costs, higher medical expenses should be justified socio-economically. Therefore, we calculated the effectiveness and cost-effectiveness of PET using the radiolabeled amino acid O-(2-[18F]-fluoroethyl)-L-tyrosine (FET) compared to conventional MRI for early identification of responders to adjuvant temozolomide chemotherapy. A recent study in IDH-wildtype glioma patients suggested that after two cycles, FET-PET parameter changes predicted a significantly longer survival while MRI changes were not significant.

MATERIALS AND METHODS

To determine the effectiveness and cost-effectiveness of serial FET-PET imaging, we analyzed published clinical data and calculated the associated costs in the context of the German healthcare system.Based on a decision-tree model, FET-PET and MRI’s effectiveness was calculated, i.e., the probability to correctly identify a responder as defined by an overall survival ≥15 months. To determine the cost-effectiveness, the incremental cost-effectiveness ratio (ICER) was calculated, i.e., the cost for each additionally identified responder by FET-PET who would have remained undetected by MRI. The robustness of the results was tested by deterministic and probabilistic (Monte Carlo simulation) sensitivity analyses.

RESULTS

Compared to MRI, FET-PET increases the rate of correctly identified responders to chemotherapy by 26%; thus, four patients need to be examined by FET-PET to identify one additional responder. Considering the respective cost for serial FET-PET and MRI, the ICER resulted in €4,396.83 for each additional correctly identified responder by FET-PET. The sensitivity analyses confirmed the robustness of the results.

CONCLUSION

In contrast to conventional MRI, the model suggests that FET PET is cost-effective in terms of ICER values. Concerning the high cost of temozolomide, the integration of FET-PET has the potential to avoid premature chemotherapy discontinuation at a reasonable cost.

Curation Guidelines for de novo Generated Transposable Element Families

Transposable elements (TEs) have the ability to alter individual genomic landscapes and shape the course of evolution for species in which they reside. Such profound changes can be understood by studying the biology of the organism and the interplay of the TEs it hosts. Characterizing and curating TEs across a wide range of species is a fundamental first step in this endeavor. This protocol employs techniques honed while developing TE libraries for a wide range of organisms and specifically addresses: (1) the extension of truncated de novo results into full-length TE families; (2) the iterative refinement of TE multiple sequence alignments; and (3) the use of alignment visualization to assess model completeness and subfamily structure. © 2021 Wiley Periodicals LLC. Basic Protocol: Extension and edge polishing of consensi and seed alignments derived from de novo repeat finders Support Protocol: Generating seed alignments using a library of consensi and a genome assembly.

POS0020 EFFICACY AND SAFETY OF SECUKINUMAB IN PATIENTS WITH ROTATOR CUFF TENDINOPATHY: A 24-WEEK, RANDOMISED, DOUBLE-BLIND, PLACEBO-CONTROLLED, PHASE II PROOF-OF-CONCEPT TRIAL

Background:

Rotator cuff tendinopathy (RC TP) is a multifactorial condition and one of the most common causes of musculoskeletal burden. Current standard of care (SoC) is limited to pain relief with NSAIDs and physiotherapy. Recent evidence indicates that IL-17A-expressing tendon-resident immune cells are present in human overuse tendinopathy, and IL-17A levels are increased in early human tendinopathic tissue samples [1, 2]. Secukinumab (SEC) is a fully human, monoclonal antibody that binds to and neutralises IL-17A.

Objectives:

To evaluate the efficacy and safety of SEC in patients with active overuse RC TP refractory to oral NSAIDs/acetaminophen, physiotherapy or corticosteroid injections.

Methods:

96 patients with symptomatic RC TP with no or <50% rupture were randomly assigned to receive seven subcutaneous injections of SEC 300 mg or placebo (PBO) at baseline and Weeks 1, 2 and 3, followed by every 4 weeks starting at Week 4. The primary endpoint was change from baseline in the Western Ontario Rotator Cuff (WORC) index score at Week 14 for SEC vs PBO (two-sided p<0.1). Secondary endpoints included, visual analogue scale (VAS) pain score, Disability of Arm, Shoulder and Hand Questionnaire (QuickDASH) score, American Shoulder and Elbow Surgeons Shoulder Evaluation Form (ASES), EQ-5D-5L score and patient global assessment (PGA) score. All endpoints were assessed through 24 weeks.

Results:

Clinically relevant improvement in both SEC and PBO groups on top of SoC treatment was observed, with no statistically significant difference demonstrated in the full study population on physical symptoms and function (Table 1). Similar results were observed in the secondary endpoints with marked improvement in both groups over time. Exploratory post-hoc analyses in a subpopulation of 39% of the study subjects with non-acute, moderate to severe disease, SEC provided significant and clinically relevant improvements vs PBO through Week 24 in total WORC score (overall treatment difference: 19.2, p <0.01) and pain (VAS, overall treatment difference: 15, p = 0.02) with early effect observed after two weeks (Figure 1). A favourable treatment effect in the more severe subgroup was demonstrated in other patient-reported outcomes. No serious adverse events were reported.

Conclusion:

Although SEC did not demonstrate a significant benefit vs PBO in the overall patient population with active overuse RC TP, SEC did provide benefit in the subpopulation with non-acute, moderate to severe disease. Larger clinical trials of SEC in this area are warranted.

References:

[1]Millar NL, et al. Sci Rep. 2016;6:27149.

[2]Millar NL, et al. Nat Rev Rheumatol.2017;13:110-122.

Table 1.

Change from baseline in the SEC versus PBO groups in WORC index and pain (VAS)

VisitSEC 300 mgPBOp-valueTotal treated population N=96WORC Index percentage score (0 worst -100 best)aDay 2922.3519.490.45Day 9937.0037.770.87Day 16943.4140.970.64Pain (VAS, 0 best - 100 worst)bDay 29−26.04−23.130.57Day 99−46.11−40.560.28Day 169−52.23−50.740.78Post-hoc population* N=37WORC Index percentage score (0 worst - 100 best)cDay 2930.0910.840.002Day 9948.2631.830.048Day 16955.9835.240.028Pain (VAS, 0 best - 100 worst)dDay 29−29.20−14.850.125Day 99−51.48−35.370.045Day 169−57.01−46.640.217

aDay 1: SEC 42.47, PBO 40.47; bSEC 67.04, PBO 64.85; cSEC 35.93, PBO 32.90, dSEC 71.72, PBO 67.58. Day 1 values are given as absolute values to describe baseline WORC/Pain status

*Post-hoc subpopulation: Baseline: (Disease duration 2-6 months) AND (WORC ≤40 OR Tear Thickness (Bauer) ≥1 OR Sein ≥2)

PBO, placebo; SEC, secukinumab; SoC, standard of care; WORC, Western Ontario Rotator Cuff Index; VAS, visual analogue scale

Figure 1.

Post-hoc analysis of function (WORC) in the treatment groups in non-acute, moderate to severe subpopulation

SEC

SE, standard error; SEC, secukinumab; WORC, Western Ontario Rotator Cuff Index

Disclosure of Interests:

Neal L Millar Grant/research support from: Honoraria or research funding from Novartis and Stryker, Iain McInnes Speakers bureau: AbbVie, Amgen, Bristol-Myers Squibb, Celgene, Janssen, Lilly, Novartis, Pfizer, and UCB, Consultant of: AbbVie, Amgen, Bristol-Myers Squibb, Celgene, Janssen, Lilly, Novartis, Pfizer, and UCB, Grant/research support from: AbbVie, Amgen, Bristol-Myers Squibb, Celgene, Janssen, Lilly, Novartis, Pfizer, and UCB, Linda Mindeholm Employee of: Employee of Novartis, Abdelkader Seroutou Employee of: Employee of Novartis, Jens Praestgaard Employee of: Employee of Novartis, Ursula Schramm Employee of: Employee of Novartis, Rafael Levitch Employee of: Employee of Novartis, Eckhard Weber Employee of: Employee of Novartis, Didier Laurent Employee of: Employee of Novartis, Jeffrey Rosen Consultant of: Research advisor for Novartis, Georg Schett Speakers bureau: Received speakers honoraria from Abbvie, Amgen, BMS, Eli Lilly, Gilead, Janssen, Novartis, UCB, Ronenn Roubenoff Employee of: Employee of Novartis, Matthias Schieker Employee of: Employee of Novartis.

1002 Calcium administration in Major haemorrhage Protocol

Introduction

Calcium gluconate is an essential part of the major haemorrhage protocol (MHP). It minimizes the exacerbation of transfusion coagulopathies due to the citrate preservative. As fifty percent of trauma patients present with hypocalcaemia prior to transfusion, the risk is pertinent. Given the importance of the issue, surprisingly current guidelines remain sparse. We analysed the percentage of patients who received calcium and their hypocalcaemia incidence.

Method

A Retrospective review of red traumas during June to August 2019. The frequency of MHP and the patient’s ionised plasma calcium levels on VBG (1.15-1.26mmol/L) were identified. Our standard stated 100% of MHP should receive calcium. A massive transfusion was defined as 10 red blood cells units in 24 hours or 4 blood products within 30mins.

Results

27 red traumas were accepted to audit, MHP was activated in 85%. Out of these 75% received calcium and on average after 6.4 units of blood products. The incidence of ionised hypocalcaemia in all MHP patients was 67%.

Conclusions

We identified a standard that supplementary calcium should be supplemented in all MHPs. Hypocalcaemia was more frequency than our research stipulated. Improvement needs to be made to meet standards. We recommend incorporation of Calcium gluconate into major haemorrhage pack and transfusion guidelines.

Abstract SP084: Replication stress response defects predict responses to ICT in non-hypermutated tumors

Immune checkpoint blockade (ICT) has provided robust, durable responses to a subset of patients. Many initial ICT trials were focused on highly mutated cancer types, such as melanoma and lung cancer, largely predicated on the idea that mutation-derived neoantigens would allow for generation of tumor-specific T cells. Subsequent analysis of patient responses in these highly mutated cancer types confirmed that increased tumor mutation burden (TMB) corresponded with improved patient outcomes. Further clinical studies identified additional predictive biomarkers, such as PD-L1 protein expression, and various gene expression signatures. Based on the success of ICT in hypermutated cancer types, further clinical trials with ICT were performed in cancers with overall lower mutational burden. These studies have indicated that many non-hypermutated cancer types with relatively low TMB may be effectively treated with ICT. For example, patients with clear cell renal cell carcinoma (ccRCC) display relatively low TMB overall, and a narrow distribution of TMB across patients, yet clinical response rates to ICT are ~30%, with some durable responses seen. Other tumor types with minimal mutation burdens, including glioblastoma (GBM) and triple negative breast cancer (TNBC), have likewise shown encouraging clinical responses to ICT. We recently demonstrated distinct tumor immunobiology between hypermutated and non-hypermutated tumor types, notably that relative neoantigen load/tumor mutation burden was only a relevant factor for immune infiltration in hypermutated tumor types. Consistent with this, clinical trials have demonstrated that TMB does not predict response to ICT in tumor types with minimal mutational load, such as breast cancer, ccRCC, and GBM. Thus, there remains a critical gap in knowledge as to how to identify which patients with non-hypermutated cancer may benefit from ICT. Here, we demonstrate that a replication stress response (RSR) defect gene expression signature accurately predicts ICT response in 11 independent non-hypermutated patient cohorts from 6 tumor types for which other biomarkers failed. Pre-clinical studies indicate that aberrant origin firing in RSR deficient tumor cells causes exhaustion of replication protein A, resulting in accumulation of immunostimulatory cytosolic DNA. Induction or suppression of RSR deficiencies was sufficient to modulate response to ICT. Taken together, the RSR defect gene signature can accurately identify patients who will benefit from ICT across numerous non-hypermutated tumor types, and pharmacological induction of RSR defects may further expand the benefits of ICT to more patients.

Citation Format: D McGrail, P Pilié, XHF Zhang, J Rosen, L Voorwerk, M Kok, A Heimberger, C Peterson, E Jonasch, S Lin. Replication stress response defects predict responses to ICT in non-hypermutated tumors [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr SP084.

Microscopic evidence for Mn-induced long range magnetic ordering in MAX phase compounds

Zero and low field nuclear magnetic resonance measurements have been performed on MAX phase samples (Cr_1-x Mn _x )₂AC with A = Ge and Ga in order to obtain local microscopic information on the nature of magnetism in this system. Our results unambiguously provide evidence for the existence of long-range magnetic order in (Cr_0.96Mn_0.04)₂GeC and for (Cr_0.93Mn_0.07)₂GaC, but not for (Cr_0.97Mn_0.03)₂GaC. We point to a possible dependence of long range magnetic order in these MAX phase compounds on the A atom.

The Dfam community resource of transposable element families, sequence models, and genome annotations

Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0-3.3 releases of Dfam ( https://dfam.org ) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam's new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.

RepeatModeler2 for automated genomic discovery of transposable element families

The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all of the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a pipeline that greatly facilitates this process. This program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE discovery. In particular, this version incorporates a module for structural discovery of complete long terminal repeat (LTR) retroelements, which are widespread in eukaryotic genomes but recalcitrant to automated identification because of their size and sequence complexity. We benchmarked RepeatModeler2 on three model species with diverse TE landscapes and high-quality, manually curated TE libraries: Drosophila melanogaster (fruit fly), Danio rerio (zebrafish), and Oryza sativa (rice). In these three species, RepeatModeler2 identified approximately 3 times more consensus sequences matching with >95% sequence identity and sequence coverage to the manually curated sequences than the original RepeatModeler. As expected, the greatest improvement is for LTR retroelements. Thus, RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/RepeatModeler, http://www.repeatmasker.org/RepeatModeler/).

Ti n+1C n MXenes with fully saturated and thermally stable Cl terminations

MXenes are a rapidly growing family of 2D materials that exhibit a highly versatile structure and composition, allowing for significant tuning of the materials properties. These properties are, however, ultimately limited by the surface terminations, which are typically a mixture of species, including F and O that are inherent to the MXene processing. Other and robust terminations are lacking. Here, we apply high-resolution scanning transmission electron microscopy (STEM), corresponding image simulations and first-principles calculations to investigate the surface terminations on MXenes synthesized from MAX phases through Lewis acidic melts. The results show that atomic Cl terminates the synthesized MXenes, with mere residual presence of other termination species. Furthermore, in situ STEM-electron energy loss spectroscopy (EELS) heating experiments show that the Cl terminations are stable up to 750 °C. Thus, we present an attractive new termination that widely expands the MXenes' functionalization space and enables new applications.

P14.18 Prognostic value of serial dynamic O-(2-[18F]-fluoroethyl)-L-tyrosine PET in patients with non-resectable malignant glioma undergoing chemoradiation

BACKGROUND

A complete resection of high-grade gliomas (HGG) is associated with improved survival, which, however, cannot be achieved in a considerable number of patients. We here evaluated the prognostic value of serial O-(2-[18F]-fluoroethyl)-L-tyrosine (FET) PET in patients with newly diagnosed, non-resectable astrocytic HGG undergoing chemoradiation with temozolomide.

MATERIAL AND METHODS

Serial dynamic FET PET scans were performed in 18 newly diagnosed patients with molecularly defined, non-resectable HGG at baseline and after chemoradiation (8±3 weeks). Both static (tumor/brain ratios, FET tumor volumes) and dynamic FET PET parameters (time-to-peak, slope), as well as MRI changes according to RANO criteria at first follow-up after chemoradiation (8±3 weeks), were obtained. The predictive ability of FET PET parameters and RANO criteria was evaluated with regard to the progression-free survival (PFS). Using ROC analyses, threshold values for FET PET parameters were obtained. Subsequently, univariate and multivariate survival analyses were performed to assess their predictive power for PFS.

RESULTS

ROC analysis revealed that the mean tumor/brain ratio (AUC, 0.84), FET tumor volume (AUC, 0.89), and slope (AUC, 0.72) at baseline were predictive for a prolonged PFS (9.3 vs. 5.7 months, P=0.05; 10.3 vs. 5.9 months; P=0.03; 13.5 vs. 6.2 months, P=0.02, respectively). Furthermore, FET tumor volume and slope remained significant in the multivariate survival analysis (both P<0.05). In contrast, relative changes of static or dynamic FET PET parameters at follow-up and MRI changes according to RANO criteria were not significant in this albeit small series of patients.

CONCLUSION

Results suggest that before initiation of chemoradiation FET PET parameters at baseline can be used to predict PFS in patients with non-resectable HGG.

A-51 A Novel Memory Catastrophizing Scale

Objective

A weak relationship exists between subjective memory complaints and performance on objective measures of learning and memory. A memory catastrophizing scale may explain this relationship. Our objective is to preliminarily explore a scale which assesses catastrophizing.

Method

The sample consisted of 46 patients (21 normal profiles, 25 mild cognitive impairment; mean age 56.1 ± 15.4) in a community-based neurology clinic. Each patient completed a clinical interview and comprehensive neuropsychological battery. The California Verbal Learning Test II (CVLT-II) was used to assess memory; the Beck Depression Inventory and Beck Anxiety Inventory were used to assess depressive and anxiety symptoms; a novel Memory Catastrophizing Scale (MCS) was used to assess subjective memory.

Results

A reliability analysis revealed internal consistency throughout the MCS (Cronbach’s alpha = .958). A bivariate correlation revealed that memory catastrophizing was significantly positively correlated with depressive (r = 0.623, p < 0.01) and anxiety (r = 0.433, p < 0.01) symptomology. Bivariate correlations demonstrated significant positive correlations between subjective memory complaints and memory (CVLT-II SDFR r = 0.502, p < .05; SDCR r = 0.434, p = 0.05; LDCR r = 0.512, p < .05) only among NP patients. The mean MCS score was 26 (±17), with a median of 17, a skewness of 0.40 and kurtosis of -0.77.

Conclusion

Our results support past research suggesting that there is a weak relationship between subjective and objective memory performances. Catastrophizing as a concept may explain the relationship between mood and performance on testing, especially amongst individuals without a known neurological pathology seeking treatment at a community-based neurological clinic.

Generation of structured light by multilevel orbital angular momentum holograms

Structured light has been created by a myriad of near-and far-field techniques and has found both classical and quantum applications. In the case of orbital angular momentum (OAM), continuous spiral phase patterns in dynamic or geometric phase are often employed with the phase patterns existing across the entire transverse plane. Here, we exploit the uncertain relationship between OAM and angle in order to create structured OAM fields by using multilevel OAM holograms. We show theoretically and experimentally that only a multilevel angular phase contour in the near-field is needed to create structured OAM light in the far-field, exploiting the reciprocal nature of angular momentum and angle. We use this approach to demonstrate exotic 3D structured light control to show the Poynting vector's evolution in such fields and to highlight the physics underlying this phenomenon.

Curriculum for neurogastroenterology and motility training: A report from the joint ANMS-ESNM task force

Although neurogastroenterology and motility (NGM) disorders are some of the most frequent disorders encountered by practicing gastroenterologists, a structured competency-based training curriculum developed by NGM experts is lacking. The American Neurogastroenterology and Motility Society (ANMS) and the European Society of Neurogastroenterology and Motility (ESNM) jointly evaluated the components of NGM training in North America and Europe. Eleven training domains were identified within NGM, consisting of functional gastrointestinal disorders, visceral hypersensitivity and pain pathways, motor disorders within anatomic areas (esophagus, stomach, small bowel and colon, anorectum), mucosal disorders (gastro-esophageal reflux disease, other mucosal disorders), consequences of systemic disease, consequences of therapy (surgery, endoscopic intervention, medications, other therapy), and transition of pediatric patients into adult practice. A 3-tiered training curriculum covering these domains is proposed here and endorsed by all NGM societies. Tier 1 NGM knowledge and training is expected of all gastroenterology trainees and practicing gastroenterologists. Tier 2 knowledge and training is appropriate for trainees who anticipate NGM disorder management and NGM function test interpretation being an important part of their careers, which may require competency assessment and credentialing of test interpretation skills. Tier 3 knowledge and training is undertaken by trainees interested in a dedicated NGM career and may be restricted to specific domains within the broad NGM field. The joint ANMS and ESNM task force anticipates that the NGM curriculum will streamline NGM training in North America and Europe and will lead to better identification of centers of excellence where Tier 2 and Tier 3 training can be accomplished.

The emergence of psychosis in a patient with severe hypothyroidism: A case report and literature review

Hypothyroidism is associated with changes in mental state that can range from mild cognitive impairment to depression to florid myxedema coma. A few cases have linked the occurence of psychotic symptoms in the context of severe hypothyroidism, an event referred in the literature as “myxedema madness”. We describe the case of a 48-year-old male with no past psychiatric history and a past medical history of hypertension and hypothyroidism who presented to the psychiatric unit for management of new-onset psychosis, particularly paranoid delusions. On basic medical screening, the patient was found to have severe hypothyroidism manifested by a TSH level of 51.85 and a free T4 level less than 0.4. The patient was treated with both an antipsychotic and thyroid hormone replacement, after which his hypothyroid symptoms and his psychosis improved. Liothyronine was also prescribed to speed up the recovery course, as his delusions were thought to be due to his hypothyroidism. The aim of this poster is to shed light on the possibility of development of psychosis concomitantly with severe hypothyroidism, given the rarity of such events, as well as to illustrate the importance of treating the underlying medical cause rather than only focusing on the treatment of the psychiatric symptoms. The use of Liothyronine proved to be beneficial in this case, as the patient's symptoms drastically improved after its administration. This could potentially illustrate the importance of using Liothyronine particularly in the treatment of delusional disorder in severe hypothyroidism.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Guidelines To Validate Control of Cross-Contamination during Washing of Fresh-Cut Leafy Vegetables

The U.S. Food and Drug Administration requires food processors to implement and validate processes that will result in significantly minimizing or preventing the occurrence of hazards that are reasonably foreseeable in food production. During production of fresh-cut leafy vegetables, microbial contamination that may be present on the product can spread throughout the production batch when the product is washed, thus increasing the risk of illnesses. The use of antimicrobials in the wash water is a critical step in preventing such water-mediated cross-contamination; however, many factors can affect antimicrobial efficacy in the production of fresh-cut leafy vegetables, and the procedures for validating this key preventive control have not been articulated. Producers may consider three options for validating antimicrobial washing as a preventive control for cross-contamination. Option 1 involves the use of a surrogate for the microbial hazard and the demonstration that cross-contamination is prevented by the antimicrobial wash. Option 2 involves the use of antimicrobial sensors and the demonstration that a critical antimicrobial level is maintained during worst-case operating conditions. Option 3 validates the placement of the sensors in the processing equipment with the demonstration that a critical antimicrobial level is maintained at all locations, regardless of operating conditions. These validation options developed for fresh-cut leafy vegetables may serve as examples for validating processes that prevent cross-contamination during washing of other fresh produce commodities.

Ti2Au2C and Ti3Au2C2 formed by solid state reaction of gold with Ti2AlC and Ti3AlC2

Ti₂Au₂C and Ti₃Au₂C₂ formation by Au/Ti₂AlC and Au/Ti₃AlC₂ exchange-reactions imply thermodynamic guidelines for identifying materials where these reactions may occur.

An investigation of the in-plane chemically ordered atomic laminates (Mo2/3Sc1/3)2AlC and (Mo2/3Y1/3)2AlC from first principles

We have calculated electronic, vibrational, and elastic properties of (Mo_2/3Sc_1/3)₂AlC and (Mo_2/3Y_1/3)₂AlC, two recently discovered nanolaminated materials in the family of so-called i-MAX phases.

Magnetic MAX phases from theory and experiments; a review

This review presents MAX phases (M is a transition metal, A an A-group element, X is C or N), known for their unique combination of ceramic/metallic properties, as a recently uncovered family of novel magnetic nanolaminates. The first created magnetic MAX phases were predicted through evaluation of phase stability using density functional theory, and subsequently synthesized as heteroepitaxial thin films. All magnetic MAX phases reported to date, in bulk or thin film form, are based on Cr and/or Mn, and they include (Cr,Mn)2AlC, (Cr,Mn)2GeC, (Cr,Mn)2GaC, (Mo,Mn)2GaC, (V,Mn)3GaC2, Cr2AlC, Cr2GeC and Mn2GaC. A variety of magnetic properties have been found, such as ferromagnetic response well above room temperature and structural changes linked to magnetic anisotropy. In this paper, theoretical as well as experimental work performed on these materials to date is critically reviewed, in terms of methods used, results acquired, and conclusions drawn. Open questions concerning magnetic characteristics are discussed, and an outlook focused on new materials, superstructures, property tailoring and further synthesis and characterization is presented.

Necrotizing Meningoencephalitis and Pneumonitis in a Simian Immunodeficiency Virus—infected Rhesus Macaque due to Acanthamoeba

Free-living amoebae of the genus Acanthamoeba can cause a fatal disease of the brain in humans called granulomatous amoebic encephalitis. We present a case of meningoencephalitis and pneumonitis in a simian immunodeficiency virus (SIV)-infected rhesus macaque caused by Acanthamoeba sp. The animal became ill 176 days after intravenous inoculation with SIVmac251 after a short history of weight loss and a sudden onset of hind limb paresis and abnormal head movements. Histopathologic examination of hematoxylin and eosin-stained tissues revealed multifocal to coalescing necrotizing neutrophilic meningoencephalitis and pneumonitis. Immunofluorescence and polymerase chain reaction were used to identify the genus of amoeba as Acanthamoeba. Immunohistochemistry of immune cell markers was used to characterize the animal's immune response to the opportunistic amoebic infection with features of both innate and adaptive cell-mediated immunity. Although not previously reported, the potential transmission to humans, either through environmental contamination or contact with an infected animal, makes this disease a threat to laboratory animal care staff and pathologists.

Phase stability of the nanolaminates V2Ga2C and (Mo1-xVx)2Ga2C from first-principles calculations

We here use first-principles calculations to investigate the phase stability of the hypothetical laminated material V₂Ga₂C and the related alloy (Mo_1–xV_x)₂Ga₂C, the latter for a potential parent material for synthesis of (Mo_1–xV_x)₂C, a new two-dimensional material in the family of so called MXenes.

We here use first-principles calculations to investigate the phase stability of the hypothetical laminated material V₂Ga₂C and the related alloy (Mo_1–xV_x)₂Ga₂C, the latter for a potential parent material for synthesis of (Mo_1–xV_x)₂C, a new two-dimensional material in the family of so called MXenes. We predict that V₂Ga₂C is thermodynamically stable with respect to all identified competing phases in the ternary V–Ga–C phase diagram. We further calculate the stability of ordered and disordered configurations of Mo and V in (Mo_1–xV_x)₂Ga₂C and predict that ordered (Mo_1–xV_x)₂Ga₂C for x ≤ 0.25 is stable, with an order–disorder transition temperature of ∼1000 K. Furthermore, (Mo_1–xV_x)₂Ga₂C for x = 0.5 and x ≥ 0.75 is suggested to be stable, but only for disordered Mo–V configurations, and only at elevated temperatures. We have also investigated the electronic and elastic properties of V₂Ga₂C; the calculated bulk, shear, and Young's modulus are 141, 94, and 230 GPa, respectively.

A theoretical investigation of mixing thermodynamics, age-hardening potential, and electronic structure of ternary M(1)1-x M(2)xB2 alloys with AlB2 type structure

Transition metal diborides are ceramic materials with potential applications as hard protective thin films and electrical contact materials. We investigate the possibility to obtain age hardening through isostructural clustering, including spinodal decomposition, or ordering-induced precipitation in ternary diboride alloys. By means of first-principles mixing thermodynamics calculations, 45 ternary M¹_1–xM²_xB₂ alloys comprising MⁱB₂ (Mⁱ = Mg, Al, Sc, Y, Ti, Zr, Hf, V, Nb, Ta) with AlB₂ type structure are studied. In particular Al_1–xTi_xB₂ is found to be of interest for coherent isostructural decomposition with a strong driving force for phase separation, while having almost concentration independent a and c lattice parameters. The results are explained by revealing the nature of the electronic structure in these alloys, and in particular, the origin of the pseudogap at E_F in TiB₂, ZrB₂, and HfB₂.

A critical evaluation of GGA + U modeling for atomic, electronic and magnetic structure of Cr2AlC, Cr2GaC and Cr2GeC

In this work we critically evaluate methods for treating electron correlation effects in multicomponent carbides using a GGA + U framework, addressing doubts from previous works on the usability of density functional theory in the design of magnetic MAX phases. We have studied the influence of the Hubbard U-parameter, applied to Cr 3d orbitals, on the calculated lattice parameters, magnetic moments, magnetic order, bulk modulus and electronic density of states of Cr2AlC, Cr2GaC and Cr2GeC. By considering non-, ferro-, and five different antiferromagnetic spin configurations, we show the importance of including a broad range of magnetic orders in the search for MAX phases with finite magnetic moments in the ground state. We show that when electron correlation is treated on the level of the generalized gradient approximation (U = 0 eV), the magnetic ground state of Cr2AC (A = Al, Ga, Ge) is in-plane antiferromagnetic with finite Cr local moments, and calculated lattice parameters and bulk modulus close to experimentally reported values. By comparing GGA and GGA + U results with experimental data we find that using a U-value larger than 1 eV results in structural parameters deviating strongly from experimentally observed values. Comparisons are also done with hybrid functional calculations (HSE06) resulting in an exchange splitting larger than what is obtained for a U-value of 2 eV. Our results suggest caution and that investigations need to involve several different magnetic orders before lack of magnetism in calculations are blamed on the exchange-correlation approximations in this class of magnetic MAX phases.

Mo2Ga2C: a new ternary nanolaminated carbide

We report the discovery of a new hexagonal Mo₂Ga₂C phase, wherein two Ga layers – instead of one – are stacked in a simple hexagonal arrangement in between Mo₂C layers.

Magnetic self-organized atomic laminate from first principles and thin film synthesis

The first experimental realization of a magnetic M(n+1)AX(n) (MAX) phase, (Cr(0.75)Mn(0.25))(2)GeC, is presented, synthesized as a heteroepitaxial single crystal thin film, exhibiting excellent structural quality. This self-organized atomic laminate is based on the well-known Cr(2)GeC, with Mn, a new element in MAX phase research, substituting Cr. The compound was predicted using first-principles calculations, from which a variety of magnetic behavior is envisaged, depending on the Mn concentration and Cr/Mn atomic configuration within the sublattice. The analyzed thin films display a magnetic signal at room temperature.

Abstract P4-02-08: Quantitative Characterization of 3D Vasculature Spatial Patterns Within Tumor Microenvironment of Breast Cancer Stem Cells

The sustainment characters of cancer stem cells (CSCs) such as self-renew and differentiation to other tumor cells greatly depend on the tumor microenvironment, which is composed of many components, e.g. vasculature, extracellular matrix, epithelial cells, stromal cells, as well as nutrients and oxygen. As vasculature is an important factor for the CSC and tumor development, the understanding of their spatial patterns is essential for calibrating the CSC-microenvironment interactions in mathematical modeling. In this study, we acquired the vasculature in side tumors and normal breast tissues by using two-photon fluorescence microscopy, which enables 3D in vivo imaging. We developed an advanced vasculature segmentation approach for an objective and accurate quantification of the vasculature in 3D image volumes. The approach integrates supervoxel analysis and the orientation guided hidden Markov random field (ori-HMRF) modeling together to compensate for low quality images, e.g., low signal-to-noise ratio (SNR) and uneven background. By constructing a new feature space that combines the CIELAB color space and the coordinates space, the supervoxel analysis divides an image volume into subregions with local similar intensity and restricted regular shape, boundaries of which can delineate the vasculature boundaries accurately even in low intensity contrast regions. We further designed a set of features for the separation of blood vessel regions from the background. To make use of the context information, i.e. the continuity of vasculature, the ori-HMRF model is used to incorporate the consistency of vasculatures' orientation in order to reduce the false positives and negatives. Experimental results on image volumes from both breast cancer and normal breast tissues show that the proposed method can effectively reconstruct the vasculature structure with the CSC embedded tumor microenvironment.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-02-08.

Abstract P5-03-08: A fluorescence STAT3 reporter preferentially expressed in human breast cancer tumor-initiating cells

Cancer initiating/stem cells are thought to be responsible for treatment-resistance, disease-recurrence and metastasis. Current breast cancer stem cell markers lack direct correlation with stem cell function, which makes the targeted therapeutic design difficult. The STAT3 pathway is a critical regulator of the function of normal stem cells and evidence is accumulating for its important role in breast cancer stem cells, as well as associated “niche” cells. However, due to lack of method for pathway-activity-based live cell separation, whether STAT3 functions in the cancer stem cells themselves or in surrounding niche cells, or both remains unknown. To answer this question, we have constructed lentiviral fluorescent reporters, which enables FACS-sorting of cells differ in STAT3 activity as well as in vivo/in situ localization of STAT3 responsive cells. Our study for the first time separated the STAT3 positive and STAT3 negative cells from the same breast tumor in live, and for the first time provided functional evidences that the STAT3 positive cells are enriched for breast cancer stem cells compared to STAT3 negative cells, as tumor cells positive for reporter activity perform better in both mammosphere formation and dilution transplantation assays compared to the negatives.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-03-08.

PD08-05: Stat3 Signaling in Human Breast Cancer Stem Cells

Recent data suggest the existence of a unique subset of breast cancer cells capable of initiating tumor growth and giving rise to all other cells characteristic of a given tumor. These cells have been termed “cancer stem cells” or “tumor-initiating cells”. Breast cancer stem cells appear to be resistant to chemo- and radiotherapies and may be responsible for recurrence and metastasis in breast cancer patients. Identifying the cellular signaling pathways responsible for breast cancer stem cell maintenance and self-renewal represents a critical hurdle for developing effective therapeutics. The Stat3 pathway is a critical regulator of the function of normal stem cells, and shows altered expression in human breast cancers [4]. Moreover, IL-6, the Stat3 signaling agonist, is required for breast cancer stem cell function in human breast cancer cell lines. All these suggest an important role of Stat3 signaling in breast cancer stem cells. However, due to lack of method for pathway-activity-based live cell separation, whether Stat3 functions in the cancer stem cells themselves or whether it may function in surrounding niche cells remain unknown. We have constructed a lentiviral fluorescent reporter for Stat3 signaling which contains four copies of M67 Stat3 binding sites upstream of enhanced Green Fluorescent Protein. This reporter system enables FACS-sorting of cells with active Stat3 signaling and in vivo/in situ localization of Stat3 responsive cells. In addition, C188-9, the first Stat3 specific competitive inhibitor, has been developed in our collaborator's lab, which provides us an advanced tool in studying Stat3 function.

We hypothesize that Stat3 signaling is preferentially active in stemlike subpopulation and depend on non-stem cancer cells to maintain its activation. Three aims to test this hypothesis include: 1. To test whether cancer cells with activated Stat3 signaling are enriched for breast cancer stem cells or whether they may serve as niche cells. 2. To test whether small molecule antagonists of Stat3 signaling can inhibit cancer stem cell function. 3. To identify novel targets of Stat3 signaling that may serve as indicators of responsiveness to Stat3 antagonist or predict treatment response.

So far, our GFP reporters for Stat3 signaling effectively report Stat3 activity in both patient xenografts and human breast cancer cell lines in vivo and in vitro, which enables effective separation of Stat3+/Stat3- cells for functional Study. MDA231 and SUM159 tumors with reporters have been established. Tumor cells will be sorted according to Stat3 activity and perform limiting dilution and MSFE assays. Tumors with reporters will also be treated by C188-9, Chemo, or in combination to study synergistic effect of Stat3 inhibitors on tumor growth. Preliminary data based on inhibitor and limiting dilution studies suggested that Stat3 signaling is required for stem cell function. However, neither Stat3+ nor Stat3- cells are self-sufficient in performing these functions, indicating communications between subpopulations.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr PD08-05.

The Role of Smoothened in Mammary Gland Development and Breast Cancer

The hedgehog (Hh) signaling pathway is a critical pathway for development and is known to influence proliferation, cell fate, morphogenesis, and stem cell self-renewal. Mutations activating Hh signaling have been found in a wide variety of cancers, and it is estimated that up to 25% of all tumors display misregulated Hh signaling. Smoothened (Smo), a seven pass transmembrane protein is the Hh signaling pathway's primary effector and its sole non-redundant member. In a recent study, Smo was found to be over-expressed in 70% of ductal carcinom in-situ (DCIS) lesions and 30% of invasive breast carcinomas (IBC). Despite the implication of this protein in breast cancer, little is known about its role in normal mammary gland development.In order to understand the role of Smo in mammary gland development we have performed phenotypic analyses of a conditional mouse model expressing constitutively activated Smo under the control of a mammary gland selective Cre recombinase. We show that activation of the Hh pathway results in increased proliferation starting around five weeks of age that leads to a dramatic increase in branching and budding of the mammary gland at around ten weeks of age. In addition, immunostaining using the ductal markers Na-K-Cl Co-transporter 1 (NKCC1) and aquaporin 5 (AQP5) suggests alterations in cell fate. Finally, these mice exhibit changes in the stroma surrounding the mammary ducts including an increase in collagen deposition. Gene profiling studies show upregulation of several genes, including targets of the Notch pathway, in ten-week-old virgin mammary glands from the constitutively active conditional Smo mouse model when compared to control. Surprisingly, canonical downstream Hh target genes like Patched and Gli were not found to be upregulated. These data in conjunction with recent published studies suggest that Smo activation in the mammary gland may be acting via a non-canonical mechanism to produce the observed hyper-branched and budded phenotype. Preliminary studies indicate that Smoothened may be functioning as a G-protein coupled receptor (GPCR) via a pertussis-toxin sensitive mechanism. Interestingly, constituitive Smo activity does not appear to alter cyclic AMP (cAMP) levels as recently reported in Drosophila indicating that mammalian Smo may be acting via a different mechanism.In addition to these gain-of-function studies, experiments are underway utilizing a conditional null Smo mouse model (loss-of-function) to determine if there is a requirement for Hh pathway activation in normal mammary gland development. Preliminary analysis indicates that partial loss of Smo in mammary gland cells leads to impaired ductal elongation and reduced branching.Future studies will include the generation of mammary gland chimeras to study the possible paracrine interactions between Smo over-expressing and wild type cells. Additionally, experiments are under way to elucidate the mechanism of Smo's GPCR function in the mammary gland.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2164.

Signal-Transduction Based Network Biomarkers for Tumor-Initiating Cells in a p53-Null Mouse Model of Breast Cancer

Introduction: Tumor initiating cells (TICs), or cancer stem cells, have the capacity to self-renew, and are likely to be responsible for resistance to conventional therapies, disease recurrence, and metastasis. Known TIC biomarkers may allow us to understand which genes are critical to self-renewal of TICs. However, little is known about how these biomarkers manipulate other molecules to enable TICs to self-renew. Here, we develop a systems biology approach to identify the signal-transduction network biomarkers for understanding the mechanisms in the renewal of TICs.Methods: Comparing with conventional biomarker discovery, the network biomarkers are identified by not only differential genes but also protein-protein interaction (PPI) network and available signaling pathways. Depending on the interacting patterns in PPI network and their associated cellular processes in signaling pathways, we can reveal the key signal transductions or subnetworks responsible for self-renewal of TICs. We chose two types of enriched interacting patterns, i.e. triangle and spoon, to indicate the signal transductions around the single biomarkers. A published RNA microarray (GSE8863) was performed on mammary epithelial cells from p53-null tumors sorted by two stem cell markers CD29 and CD24. The differential genes were identified by the Fold-Changes (FCs) comparing the subpopulations of Lin —CD29HCD24H with other subpopulations. Gene Set Enrichment Analysis (GSEA) revealed that the identified differential genes are significantly enriched in 20 regulatory pathways including 'Cell cycle', 'Adherens junction', 'Cell adhesion molecules (CAMs)', 'Tight junction' (P&lt;10-3). A model called Multiple Objective Optimization (MOO) was employed to search the network biomarkers whose component proteins satisfy that (1) be most differentially expressed in Lin —CD29HCD24H cells and (2) pass through a large number of enriched signaling pathways.Results: Four genes (Lsm5, Calm3, Bmi1 and Ezh2) are extremely up-regulated in the Lin —CD29HCD24H subpopulations (FC&gt;4), in which Bmi1 is important in regulating the self-renewal capacity of hematopoietic, as well as human mammary gland stem cells. To understand how these genes manipulate other genes and the enriched signaling pathways, we first analyzed the interacting patterns around these genes. Calm3 and Bmi1 are surrounded by 355 and 22 interacting patterns respectively. The component coding-genes in the interacting patterns are more likely to be differentially expressed (91/127, P &lt;10-61). Then, the protein-paths were identified from the interacting patterns of Calm3 and Bmi1 by MOO. IPA (Ingenuity Pathway Analysis) indicated that these protein paths have many particular cellular functions related to self-renewal, such as 'Cell Growth and Proliferation', 'Hematological System Development and Function', 'Cell-To-Cell Signaling and Interaction', and 'Cell Death' (P &lt;10-3).Conclusion: The network biomarkers revealed that the surrounding interaction patterns and related signaling pathways of single biomarkers are essential to understand the signal-transduction mechanisms of TICs in self-renewal. They may be useful as prognostic or predictive indicators as well as suggest possible targets for novel therapies.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2138.

Hyperthermia Sensitizes Breast Cancer Stem Cells to Radiation Therapy

Background In cancer, metastatic disease and recurrence are hypothesized to result, at least in part, from the residual cancer stem cells (CSCs), also referred to as tumor-initiating cells(TICs), which evade initial treatment. In several genetically engineered mouse models that resemble human breast cancer, the tumor subpopulation CD29+/CD24+/lin- has been shown to be more tumorigenic as compared to other subpopulations by in vitro and in vivo assays. We and others have demonstrated that the tumorigenic CD29+/CD24+/lin- subpopulation repairs radiation-induced DNA strand breaks more efficiently than the other subpopulations. Therefore, we hypothesized that hyperthermia, a documented means of inhibiting DNA repair, may radiosensitize CSCs to radiation therapy(RT) by delaying and inhibiting the repair of DNA strand breaks. Methods To test this hypothesis, we assayed for tumorigenic CD29+/CD24+/lin- cells in p53null mouse mammary tumor model with and without radiation, and in combination with hyperthermia (42°C) administered as optically-activated gold nanoparticles. We then determined if there was a decrease in functional CSCs by FACS analysis and limiting dilution transplantation assays. Results These studies confirmed that CD29+/CD24+/lin- cells were more radiation resistant and that their relative proportion was increased after RT, as compared to the other cell populations. However, the addition of hyperthermia increased the sensitivity of the CD29+/CD24+/lin- subpopulation to radiation. Radiation treatment alone in vivo resulted in a decrease in tumor size, but the percentage of tumorigenic cells increased as compared to untreated controls. In contrast, following post-treatment with 20 minutes of local hyperthermia, using intravenously administered optically activated gold nanoparticles, a larger regression in tumor size was observed, without a concomitant increase in the percentage of CD29+/CD24+/lin- tumorigenic cells. Using the functional limiting dilution transplantation assay to assay for CSCs, we showed that 48 hours after treatment cells derived from tumors treated with RT exhibited an increased frequency of TICs as compared to untreated controls, and tumors treated with radiation and hyperthermia. In addition, clonogenic survival assays of this tumorigenic subpopulation had consistent results with the in vivo data. Conclusion These results suggest that localized hyperthermia serves as a simple strategy to selectively sensitize the radioresistant subpopulation of CSCs to enhance their response to radiation therapy. The mechanisms responsible for these effects of hyperthermia are currently under investigation. Supported by grant NCI R01 CA112305 and CA16303.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 506.