Novel WRN Helicase Inhibitors Selectively Target Microsatellite Unstable Cancer Cells

Microsatellite-unstable (MSI) cancers require WRN helicase to resolve replication stress due to expanded DNA (TA)n-dinucleotide repeats. WRN is a promising synthetic lethal target for MSI tumours, and WRN inhibitors are in development. Here, we used CRISPR-Cas9 base editing to map WRN residues critical for MSI cells, validating the helicase domain as the primary drug target. Fragment-based screening led to the development of potent and highly selective WRN helicase covalent inhibitors. These compounds selectively suppressed MSI model growth In vitro and In vivo by mimicking WRN loss, inducing DNA double-strand breaks at expanded TA-repeats and DNA damage. Assessment of biomarkers in preclinical models linked TA-repeat expansions and mismatch repair (MMR) alterations to compound activity. Efficacy was confirmed in immunotherapy-resistant organoids and patient-derived xenograft (PDX) models. The discovery of potent, selective covalent WRN inhibitors provides proof of concept for synthetic-lethal targeting of WRN in MSI cancer and tools to dissect WRN biology.

Biomarker discovery and authentication of cold-slaughtered chicken through classical analytical procedures and mass spectrometry based proteomic approaches

1. This study evaluated the suitability of routine analytical procedures and used mass spectrometry-based proteomic approaches to distinguish meat from dead chicken/ cold-slaughtered birds (CS), electrically stunned and slaughtered birds, as per standard protocols (ES), and birds slaughtered according to halal guidelines (HS).2. Meat from CS birds had lower (P < 0.05) pH, water-holding capacity and higher (P < 0.05) lipid oxidation, haem iron content, residual blood and total viable counts relative to ES and HS meat indicating poor quality.3. The results demonstrated the presence of unique protein bands on SDS-PAGE only in CS meat that can be used for routine screening.4. Protein analysis using MALDI-TOF mass spectrometry identified haemoglobin subunit alpha-A and alpha-D; Adenylate kinase isoenzyme 1 as reliable and stable marker proteins for authentication of dead chicken meat under raw and cooked conditions and halal slaughtered chicken, respectively.5. The methods used may be employed by the food safety and regulatory agencies for regular screening of meat quality and to authenticate CS or HS chicken.

Management of idiopathic granulomatous mastitis: a prospective study

INTRODUCTION

Idiopathic granulomatous mastitis (IGM) is an evolving problem with varied presentation. No definite treatment guidelines are available at present that may reduce rate of recurrence. Current evidence suggests a ductal pathology behind IGM, which leads to periductal mastitis, leakage and sinus/fistula formation. Thus, excision of the sinus/fistulous tract with en-bloc wide local excision (WLE) of the lesion could be curative. The objective of this study was to look for the basic aetiology of IGM and evaluate the effectiveness of WLE with total or partial duct excision as a curative approach.

METHODS

An institutional prospective comparative study was conducted over 4 years (2015-2019), in which 59 cases of IGM were randomly divided into three groups. After necessary investigations, patients in group A received steroid therapy, those in group B received WLE and patients in group C received WLE with total or partial duct excision as the mode of treatment. Postoperative follow-up was between 6 months and 3 years.

RESULTS

Histopathological examination (HPE) was found to be the most suitable diagnostic procedure. Patients in group B showed the highest rate of recurrence (73.6%), followed by group A (35.0%) and group C (5.0%). Patients in group C had a significantly lower chance of recurrence compared with both group A and group B (p < 0.05). HPE reports of excised ducts from patients in group C showed ductal disruption and leakage along with periductal granuloma in 70% of cases.

CONCLUSIONS

The presence of duct granuloma indicates the association of ductal pathology in IGM. IGM is therefore a disease of the mammary ducts and en-bloc duct excision is curative in non-responding cases.

Heavy metal deposition temperature tuned spin pumping efficiency control in permalloy/tantalum bilayers

Spin pumping is a key property for spintronic application that can be realized in heavy metal/ferromagnet bilayers. Here we demonstrate the possibility of improving spin pumping in permalloy (Py)/tantalum (Ta) bilayers through control of Ta heavy metal deposition temperature. Through a combination of structural and ferromagnetic resonance based magnetization dynamics study, we reveal the role of Ta deposition temperature in improving spin mixing conductance which is a key parameter for spin pumping across the Py/Ta interface. The results show that by depositing Ta above room temperature, a high spin mixing conductance of 7.7 ×10¹⁸m^-2is obtained withα-Ta layer. The results present an understanding of the correlation between heavy metal deposition temperature and interface structure improvement and consequent control of spin pumping in Py/Ta bilayers.

Chromosomal instability (CIN) in HAP1 cell lines revealed by multiplex fluorescence in situ hybridisation (M-FISH)

BACKGROUND

HAP1, a near-haploid human leukemic cancer cell line is often used in combination with CRISPR-Cas9 gene editing technology for genetic screens. HAP1 carries the Philadelphia chromosome (Ph) and an additional ~ 30 Mb fragment of chromosome 15 inserted into chromosome 19. The potential use of an in vitro cell line as a model system in biomedical research studies depends on its ability to maintain genome stability. Being a cancer cell line with a near-haploid genome, HAP1 is prone to genetic instability, which is further compounded by its tendency to diploidise in culture spontaneously. Moreover, CRISPR-Cas9 gene editing coupled with prolonged in-vitro cell culturing has the potential to induce unintended 'off-target' cytogenetic mutations. To gain an insight into chromosomal instability (CIN) and karyotype heterogeneity, 19 HAP1 cell lines were cytogenetically characterised, 17 of which were near-haploids and two double-haploids, using multiplex fluorescence in situ hybridisation (M-FISH), at single cell resolution. We focused on novel numerical (N) and structural (S) CIN and discussed the potential causal factors for the observed instability. For each cell line we examined its ploidy, gene editing status and its length of in-vitro cell culturing.

RESULTS

Sixteen of the 19 cell lines had been gene edited with passage numbers ranging from 10 to 35. Diploidisation in 17 near-haploid cell lines ranged from 4 to 35% and percentage of N- and S-CIN in [1n] and [2n] metaphases ranged from 7 to 50% with two cell lines showing no CIN. Percentage of cells with CIN in the two double-haploid cell lines were 96% and 100% respectively. The most common S-CIN observed was deletion followed by translocation of both types, non-reciprocal and Robertsonian. Interestingly, we observed a prevalence of S-CIN associated with chromosome 13 in both near-and double-haploid cell lines, with a high incidence of Robertsonian translocation involving chromosome 13. Furthermore, locus-specific BAC (bacterial artificial chromosome) FISH enabled us to show for the first time that the additional chromosome 15 fragment is inserted into the p-arm rather than the q-arm of chromosome 19 of the HAP1 genome.

CONCLUSION

Our study revealed a high incidence of CIN leading to karyotype heterogeneity in majority of the HAP1 cell lines with the number of chromosomal aberrations varying between cell lines. A noteworthy observation was the high frequency of structural chromosomal aberrations associated with chromosome 13. We showed that CRISPR-Cas9 gene editing technology in combination with spontaneous diploidisation and prolonged in-vitro cell culturing is potentially instrumental in inducing further chromosomal rearrangements in the HAP1 cell lines with existing CIN. We highlight the importance of maintaining cell lines at low passage and the need for regular monitoring to prevent implications in downstream applications. Our study also established that the additional fragment of chromosome 15 in the HAP1 genome is inserted into chromosome 19p rather than 19q.

'Stat' workflow modifications to expedite care after needlestick injuries

BACKGROUND

Post-exposure prophylaxis (PEP) for human immunodeficiency virus (HIV) is recommended to start within hours of needlestick injuries (NSIs) among healthcare workers (HCWs). Delays associated with awaiting the results of testing from the source patient (whose blood was involved in the NSI) can lead to psychological consequences for the exposed HCW as well as symptomatic toxicities from empiric PEP.

AIMS

After developing a 'stat' (immediate) workflow that prioritized phlebotomy and resulting of source patient bloodwork for immediate handling and processing, we retrospectively investigated whether our new workflow had (i) decreased HIV order-result interval times for source patient HIV bloodwork and (ii) decreased the frequency of HIV PEP prescriptions being dispensed to exposed HCWs.

METHODS

We retrospectively analysed NSI records to identify source patient HIV order-result intervals and PEP dispensing frequencies across a 6-year period (encompassing a 54-month pre-intervention period and 16-month post-intervention period).

RESULTS

We identified 251 NSIs, which occurred at similar frequencies before versus after our intervention (means 3.54 NSIs and 3.75 NSIs per month, respectively). Median HIV order-result intervals decreased significantly (P < 0.05) from 195 to 156 min after our intervention, while the proportion of HCWs who received one or more doses of PEP decreased significantly (P < 0.001) from 50% (96/191) to 23% (14/60).

CONCLUSION

Using a 'stat' workflow to prioritize source patient testing after NSIs, we achieved a modest decrease in order-result intervals and a dramatic decrease in HIV PEP dispensing rates. This simple intervention may improve HCWs' physical and psychological health during a traumatic time.

Werner Helicase Is a Synthetic-Lethal Vulnerability in Mismatch Repair-Deficient Colorectal Cancer Refractory to Targeted Therapies, Chemotherapy, and Immunotherapy

Targeted therapies, chemotherapy, and immunotherapy are used to treat patients with mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) colorectal cancer. The clinical effectiveness of targeted therapy and chemotherapy is limited by resistance and drug toxicities, and about half of patients receiving immunotherapy have disease that is refractory to immune checkpoint inhibitors. Loss of Werner syndrome ATP-dependent helicase (WRN) is a synthetic lethality in dMMR/MSI-H cells. To inform the development of WRN as a therapeutic target, we performed WRN knockout or knockdown in 60 heterogeneous dMMR colorectal cancer preclinical models, demonstrating that WRN dependency is an almost universal feature and a robust marker for patient selection. Furthermore, models of resistance to clinically relevant targeted therapy, chemotherapy, and immunotherapy retain WRN dependency. These data show the potential of therapeutically targeting WRN in patients with dMMR/MSI-H colorectal cancer and support WRN as a therapeutic option for patients with dMMR/MSI-H cancers refractory to current treatment strategies. SIGNIFICANCE: We found that a large, diverse set of dMMR/MSI-H colorectal cancer preclinical models, including models of treatment-refractory disease, are WRN-dependent. Our results support WRN as a promising synthetic-lethal target in dMMR/MSI-H colorectal cancer tumors as a monotherapy or in combination with targeted agents, chemotherapy, or immunotherapy.This article is highlighted in the In This Issue feature, p. 1861.

Nonreciprocal Transport of Exciton Polaritons in a Non-Hermitian Chain

We consider exciton polaritons in a zigzag chain of coupled elliptical micropillars subjected to incoherent excitation. The driven-dissipative nature of the system along with the naturally present polarization splitting inside the pillars gives rise to nonreciprocal dynamics, which eventually leads to the non-Hermitian skin effect, where all the modes of the system collapse to one edge. As a result, the polaritons propagate only in one direction along the chain, independent of the excitation position, and the propagation in the opposite direction is suppressed. The system shows robustness against disorder and, using the bistable nature of polaritons to encode information, we show one-way information transfer. This paves the way for compact and robust feedback-free one-dimensional polariton transmission channels without the need for external magnetic field, which are compatible with proposals for polaritonic circuits.

Correction to: PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas

An amendment to this paper has been published and can be accessed via the original article.

PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas

Background

Glioma is the most common intrinsic brain tumor and also occurs in the spinal cord. Activating EGFR mutations are common in IDH1 wild-type gliomas. However, the cooperative partners of EGFR driving gliomagenesis remain poorly understood.

Results

We explore EGFR-mutant glioma evolution in conditional mutant mice by whole-exome sequencing, transposon mutagenesis forward genetic screening, and transcriptomics. We show mutant EGFR is sufficient to initiate gliomagenesis in vivo, both in the brain and spinal cord. We identify significantly recurrent somatic alterations in these gliomas including mutant EGFR amplifications and Sub1, Trp53, and Tead2 loss-of-function mutations. Comprehensive functional characterization of 96 gliomas by genome-wide piggyBac insertional mutagenesis in vivo identifies 281 known and novel EGFR-cooperating driver genes, including Cdkn2a, Nf1, Spred1, and Nav3. Transcriptomics confirms transposon-mediated effects on expression of these genes. We validate the clinical relevance of new putative tumor suppressors by showing these are frequently altered in patients’ gliomas, with prognostic implications. We discover shared and distinct driver mutations in brain and spinal gliomas and confirm in vivo differential tumor suppressive effects of Pten between these tumors. Functional validation with CRISPR-Cas9-induced mutations in novel genes Tead2, Spred1, and Nav3 demonstrates heightened EGFRvIII-glioma cell proliferation. Chemogenomic analysis of mutated glioma genes reveals potential drug targets, with several investigational drugs showing efficacy in vitro.

Conclusion

Our work elucidates functional driver landscapes of EGFR-mutant gliomas, uncovering potential therapeutic strategies, and provides new tools for functional interrogation of gliomagenesis.

RAP1-RAC1 Signaling Has an Important Role in Adhesion and Migration in HNSCC

Cell-cell adhesion is a key mechanism to control tissue integrity and migration. In head and neck squamous cell carcinoma (HNSCC), cell migration facilitates distant metastases and is correlated with poor prognosis. RAP1, a ras-like protein, has an important role in the progression of HNSCC. RAC1 is an integrin-linked, ras-like protein that promotes cell migration. Here we show that loss of cell-cell adhesion is correlated with inactivation of RAP1 confirmed by 2 different biochemical approaches. RAP1 activation is required for cell-matrix adhesion confirmed by adhesion to fibronectin-coated plates with cells that have biochemically activated RAP1. This effect is reversed when RAP1 is inactivated. In addition, RAP1_GTP-mediated adhesion is only facilitated through α5β1 integrin complex and is not a function of either α5 or β1 integrin alone. Moreover, the inside-out signaling of RAP1 activation is coordinated with RAC1 activation. These findings show that RAP1 has a prominent role in cell-matrix adhesion via extracellular matrix molecule fibronectin-induced α5β1 integrin and supports a critical role for the RAP1/RAC1 signaling axis in HNSCC cell migration.

Coupling between Exciton-Polariton Corner Modes through Edge States

Recently realized higher order topological insulators have taken a surge of interest among the theoretical and experimental condensed matter community. The two-dimensional second order topological insulators give rise to zero-dimensional localized corner modes that reside within the band gap of the system along with edge modes that inhabit a band edge next to bulk modes. Thanks to the topological nature, information can be trapped at the corners of these systems, which will be unhampered even in the presence of disorder. Being localized at the corners, the exchange of information among the corner states is an issue. Here we show that the nonlinearity in an exciton polariton system can allow the coupling between the different corners through the edge states based on optical parametric scattering, realizing a system of multiple connectible topological modes.

Analysis pipelines for cancer genome sequencing in mice

Mouse models of human cancer have transformed our ability to link genetics, molecular mechanisms and phenotypes. Both reverse and forward genetics in mice are currently gaining momentum through advances in next-generation sequencing (NGS). Methodologies to analyze sequencing data were, however, developed for humans and hence do not account for species-specific differences in genome structures and experimental setups. Here, we describe standardized computational pipelines specifically tailored to the analysis of mouse genomic data. We present novel tools and workflows for the detection of different alteration types, including single-nucleotide variants (SNVs), small insertions and deletions (indels), copy-number variations (CNVs), loss of heterozygosity (LOH) and complex rearrangements, such as in chromothripsis. Workflows have been extensively validated and cross-compared using multiple methodologies. We also give step-by-step guidance on the execution of individual analysis types, provide advice on data interpretation and make the complete code available online. The protocol takes 2-7 d, depending on the desired analyses.

Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening

Many gene fusions are reported in tumours and for most their role remains unknown. As fusions are used for diagnostic and prognostic purposes, and are targets for treatment, it is crucial to assess their function in cancer. To systematically investigate the role of fusions in tumour cell fitness, we utilized RNA-sequencing data from 1011 human cancer cell lines to functionally link 8354 fusion events with genomic data, sensitivity to >350 anti-cancer drugs and CRISPR-Cas9 loss-of-fitness effects. Established clinically-relevant fusions were identified. Overall, detection of functional fusions was rare, including those involving cancer driver genes, suggesting that many fusions are dispensable for tumour fitness. Therapeutically actionable fusions involving RAF1, BRD4 and ROS1 were verified in new histologies. In addition, recurrent YAP1-MAML2 fusions were identified as activators of Hippo-pathway signaling in multiple cancer types. Our approach discriminates functional fusions, identifying new drivers of carcinogenesis and fusions that could have clinical implications.

Gene fusions are observed in many cancers but their link to tumour fitness is largely unknown. Here, transcriptomic analysis combined with pharmacological and CRISPR-Cas9 screening of cancer cell lines was used to evaluate the functional linkage between fusions and tumour fitness.

PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice

B-cell lymphoma (BCL) is the most common hematologic malignancy. While sequencing studies gave insights into BCL genetics, identification of non-mutated cancer genes remains challenging. Here, we describe PiggyBac transposon tools and mouse models for recessive screening and show their application to study clonal B-cell lymphomagenesis. In a genome-wide screen, we discover BCL genes related to diverse molecular processes, including signaling, transcriptional regulation, chromatin regulation, or RNA metabolism. Cross-species analyses show the efficiency of the screen to pinpoint human cancer drivers altered by non-genetic mechanisms, including clinically relevant genes dysregulated epigenetically, transcriptionally, or post-transcriptionally in human BCL. We also describe a CRISPR/Cas9-based in vivo platform for BCL functional genomics, and validate discovered genes, such as Rfx7, a transcription factor, and Phip, a chromatin regulator, which suppress lymphomagenesis in mice. Our study gives comprehensive insights into the molecular landscapes of BCL and underlines the power of genome-scale screening to inform biology.

Reference range of liver corrected T1 values in a population at low risk for fatty liver disease-a UK Biobank sub-study, with an appendix of interesting cases

Purpose

Corrected T1 (cT1) value is a novel MRI-based quantitative metric for assessing a composite of liver inflammation and fibrosis. It has been shown to distinguish between non-alcoholic fatty liver disease (NAFL) and non-alcoholic steatohepatitis. However, these studies were conducted in patients at high risk for liver disease. This study establishes the normal reference range of cT1 values for a large UK population, and assesses interactions of age and gender.

Methods

MR data were acquired on a 1.5 T system as part of the UK Biobank Imaging Enhancement study. Measures for Proton Density Fat Fraction and cT1 were calculated from the MRI data using a multiparametric MRI software application. Data that did not meet quality criteria were excluded from further analysis. Inter and intra-reader variability was estimated in a set of data. A cohort at low risk for NAFL was identified by excluding individuals with BMI ≥ 25 kg/m² and PDFF ≥ 5%. Of the 2816 participants with data of suitable quality, 1037 (37%) were classified as at low risk.

Results

The cT1 values in the low-risk population ranged from 573 to 852 ms with a median of 666 ms and interquartile range from 643 to 694 ms. Iron correction of T1 was necessary in 36.5% of this reference population. Age and gender had minimal effect on cT1 values.

Conclusion

The majority of cT1 values are tightly clustered in a population at low risk for NAFL, suggesting it has the potential to serve as a new quantitative imaging biomarker for studies of liver health and disease.

Abstract 391: Evolutionary trajectories and KRAS gene dosage define pancreatic cancer phenotypes

Pancreatic ductal adenocarcinoma (PDAC) has frequent alterations in few genes (KRAS, CDKN2A/TP53/SMAD4) and extensive heterogeneity of cancer drivers beyond. The expectation that mutational landscapes of rare drivers could explain phenotypic diversity has -with few exceptions- not come true. Likewise, PDAC metastasis is not understood, and comparisons of primary/metastasis pairs did not find recurrently mutated “metastasis genes”. Here we show that key aspects of PDAC biology are defined by gene-dosage variation of PDAC signature genes, evolving along distinct evolutionary routes. We found increased gene dosage of the initiating KRAS mutation (KRASMUT-iGD) in human PDAC precursors. Mouse models revealed the importance of KrasMUT-iGD for both, early progression and metastasis, rationalizing the high frequency of PDAC dissemination at diagnosis. To overcome limitations posed to gene dosage studies by PDAC´s stroma-richness, we developed murine cell culture resources comprising 135 primaries/metastases. Integrative analyses of their genomes, transcriptomes and tumor phenotypes, combined with human studies and functional analyses revealed a series of additional KrasMUT-dosage effects: different KrasMUT-levels define distinct cellular morphologies, histopathologies and clinical outcomes, with highest KrasMUT-expression underlying the most aggressive undifferentiated phenotypes. We also observed KrasMUT-dosage-associated cellular plasticity, including epithelial-to-mesenchymal transition. Mechanistically, oncogenic dosage-variation is linked to distinct evolutionary routes, characterized by defined types/states of tumor-suppressor alterations: Phylogenetic tracking studies revealed convergent evolution of KrasMUT-iGD-gains, with dependence on prior homozygous Cdkn2a- or Trp53-loss. By contrast, in Cdkn2aHET cancers, amplifications of known and novel oncogenes (Myc, Yap1, Nfkb2) collaborate with KrasMUT-HET to drive progression, yet with lower metastatic potential. These results also reveal oncogene-selective/context-dependent Cdkn2a-haploinsufficiency, for which Tgfβ pathway alterations provide permissiveness. Our study uncovers universal principles underlying PDAC biology and phenotypic diversification. It describes evolutionary trajectories, identifies their genetic hallmarks and shows how oncogenic dosage-variation is differentially licensed along individual routes to control critical disease characteristics, including early progression, histopathology, metastasis, cellular plasticity and clinical aggressiveness.

Citation Format: Sebastian Mueller, Thomas Engleitner, Roman Maresch, Magdalena Zukowska, Sebastian Lange, Thorsten Kaltenbacher, Björn Konukiewitz, Rupert Öllinger, Maximilian Zwiebel, Alex Strong, Hsi-Yu Yen, Ruby Banerjee, Sandra Louzada, Beiyuan Fu, Barbara Seidler, Juliana Götzfried, Kathleen Schuck, Zonera Hassan, Nina Schönhuber, Sabine Klein, Christian Veltkamp, Mathias Friedrich, Lena Rad, Maxim Barenboim, Christoph Ziegenhain, Julia Hess, Oliver M. Dovey, Stefan Eser, Swati Parekh, Fernando Constantino-Casas, Jorge de la Rosa, Marta I. Sierra, Mario Fraga, Julia Mayerle, Günter Klöppel, Roland M. Schmid, Juan Cadiñanos, Pentao Liu, George Vassiliou, Wilko Weichert, Katja Steiger, Wolfgang Enard, Fengtang Yang, Kristian Unger, Günter Schneider, Ignacio Varela, Allan Bradley, Dieter Saur, Roland Rad. Evolutionary trajectories and KRAS gene dosage define pancreatic cancer phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 391.

Isolation and Purification of a Coagulant from Snake Venom of the Species Bothrops jararaca and the Study of its Properties

1. A material active in coagulating fibrinogen has been purified thirty-fold from crude venom of the species Bothrops jararaca. This material exhibits clotting and esterase activities, but no measurable proteolytic activity if measured by its ability to digest denatured hemoglobin.

2. The clotting activity of the purified material (but not its esterase activity) is greatly enhanced by the addition of 2—3 μM of calcium ion; no other divalent metallic ion can duplicate the accelerating effect of Ca++ ion.

3. The purified material is stable to dialysis, standing at room temperature for 18—20 hours, or heating at 50° C for 10 minutes; it loses both its clotting and esterase activities if heated at 70° C for 25 minutes or at 80° C for 10 minutes

4. Although the powerful proteolytic enzyme inhibitors ovomucoid and soyabean trypsin inhibitor can block the clotting and esterase activities of thrombin, they are ineffective with respect to these properties of venom-coagulin. DFP, an inhibitor of far less specificity, can prevent the actions both of thrombin and of venom-coagulin

5. An amount of heparin sufficient to block the clotting activity of thrombin is unable to prevent the action of venom-coagulin on fibrinogen; a much higher concentration of heparin is needed. In both cases the addition of 2—3 μM of Ca++ ion necessitates the introduction of considerably more heparin in order to block the actions of thrombin and venom-coagulin.

6. While the antithrombin contained in serum can neutralize the clotting and esterase activities of thrombin, it has no effect on the actions of venom-coagulin.

ANITA-An active vibration cancellation system for scanning probe microscopy

The high sensitivity of scanning probe microscopes poses a barrier to their use in noisy environments. Vibrational noise, whether from structural or acoustic sources, can manifest as relative motion between the probe tip and sample, which then appears in the probe position ("Z") feedback as it tries to cancel this motion. Here we describe an active cancellation process that nullifies the appearance of this vibration by adding a drive signal into the existing Z-feedback loop. The drive is digitally calculated from accelerometer-based vibration measurements. By transferring the vibration cancellation effort to this drive signal, vibration-created noise is significantly reduced. This inexpensive and easy solution requires no major instrumental modifications and is ideal for those looking to place their microscopes in noisier environments, coupled, for example, to active refrigeration systems (e.g., pulse tube cryocoolers) or other high-vibration instruments.

Risk factors for diagnostic delay in Crohn's disease and their impact on long-term complications: how do they differ in a tuberculosis endemic region?

BACKGROUND

The diagnosis of Crohn's disease (CD) can be delayed in clinical practice. In tuberculosis endemic areas, empirical anti-tubercular therapy further delays treatment.

AIM(S)

To assess risk factors for diagnostic delay and its impact on the long-term complications of Crohn's disease in India where tuberculosis is endemic.

METHODS

Data from a large prospectively established inflammatory bowel disease registry were analysed retrospectively. The time from onset of symptoms to diagnosis (diagnostic delay) was calculated and categorised into two groups based on median diagnostic delay. The risk factors for delay including anti-tubercular therapy were analysed. Logistic regression analysis was done to assess impact of diagnostic delay on development of stenotic and fistular complications including need for surgery.

RESULTS

Seven hundred and twenty Crohn's disease patients (60.3% male, median: 28 years) were included. Main outcome measures were stenosis, fistula and need for surgery. Subjects with diagnostic delay >18 months (median) developed significantly higher stenotic complications and surgery (OR 4.12; 95% CI: 2.74-6.33, P < 0.001 and OR 2.41, 95% CI: 1.68-3.42, P < 0.001), respectively, compared to those ≤18 months. There was no difference in the development of fistulous complications. 193/720 (27%) received anti-tubercular therapy which significantly contributed to diagnostic delay (OR: 2.47; 95% CI: 1.76-3.47, P < 0.001) with 47% showing initial clinical response (Crohn's disease activity index- CDAI decrease >100). Moreover, the incidence of stenotic complications was significantly higher in patients who had received prior anti-tubercular therapy (55/193 (28.49%) vs 78/527 (14.8%), P < 0.001, OR: 2.60, 95% CI: 1.64-4.12).

CONCLUSIONS

Diagnostic delay in Crohn's disease is associated with significantly higher stenotic complications and need for surgery. Empirical anti-tubercular therapy is the single largest contributor to diagnostic delay in tuberculosis endemic areas. Despite initial clinical response to anti-tubercular therapy, long-term stenotic complications are higher.

Measurement of Hemodynamic and Anatomic Parameters in a Swine Arteriovenous Fistula Model

Purpose

Although arteriovenous fistulae (AVFs) are currently the preferred mode of permanent hemodialysis access they do have significant problems due to initial non-maturation and a later venous stenosis. These problems appear to have been exacerbated following a push to increase AVF prevalence in the US. The reasons for both AVF non-maturation and the later venous stenoses are unclear but are thought to be related to abnormal hemodynamic wall shear stress (WSS) profiles. This technical note aims to describe the successful development of measurement techniques that can be used to establish a complete hemodynamic profile in a pig model with two different configurations of AVF.

Methods and results

The curved and straight AVF configurations were created in an in vivo pig model. Flow and pressure in the AVFs were measured using the perivascular flow probes and Doppler flow wires while the pressure was recorded using a pressure transducer. The anatomical configuration was obtained using two different approaches: a) combination of intravascular ultrasound (IVUS) and angiograms, (b) 64 slice CT angiography. 3D models were reconstructed using image processing and computer modeling techniques. Numerical calculations were then performed by applying the measured flow and pressure data into the configurations to obtain the hemodynamic WSS profiles.

Conclusion

The described methodologies will allow the calculation and optimization of WSS profiles in animal models. This information could then be translated to the clinical setting where it would have a positive impact on improving the early maturation rates of AVFs as well as reducing the late venous stenoses.

Controversies in tuberculous infection among pediatric infectious disease specialists in North America

OBJECTIVE

To evaluate the extent to which advancements in the diagnosis and treatment of latent tuberculous infection (LTBI) have been integrated into practice by pediatric infectious disease (PID) specialists.

DESIGN

We conducted an online survey of the Infectious Diseases Society of America's Emerging Infections Network (EIN) membership.

RESULTS

Of the 323 members, 197 (61%) responded: 7% cared for ⩾5 children with TB disease and 34% for ⩾5 children with LTBI annually. We identified substantial variations in the use of interferon-gamma release assays (IGRAs) based upon age, immune status, and TB risk factors. In addition, tuberculin skin test (TST) use was three times more common in younger children. Variations existed in managing children with discordant TST and IGRA results. Less variation existed in LTBI treatment, with 86% preferring a 9-month course of isoniazid; few other, newer regimens were used routinely.

CONCLUSION

Substantial variations exist in LTBI management; uptake of newer diagnostic tools and treatment regimens has been slow. Variations in practice and the lag time to integrating new data into practice may indicate the relative infrequency with which providers encounter LTBI. Our findings reflect the need for increased visibility of existing TB guidelines and resources for expert consultation for scenarios not covered by guidelines.

Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

The poor correlation of mutational landscapes with phenotypes limits our understanding of the pathogenesis and metastasis of pancreatic ductal adenocarcinoma (PDAC). Here we show that oncogenic dosage-variation has a critical role in PDAC biology and phenotypic diversification. We find an increase in gene dosage of mutant KRAS in human PDAC precursors, which drives both early tumorigenesis and metastasis and thus rationalizes early PDAC dissemination. To overcome the limitations posed to gene dosage studies by the stromal richness of PDAC, we have developed large cell culture resources of metastatic mouse PDAC. Integration of cell culture genomes, transcriptomes and tumour phenotypes with functional studies and human data reveals additional widespread effects of oncogenic dosage variation on cell morphology and plasticity, histopathology and clinical outcome, with the highest KrasMUT levels underlying aggressive undifferentiated phenotypes. We also identify alternative oncogenic gains (Myc, Yap1 or Nfkb2), which collaborate with heterozygous KrasMUT in driving tumorigenesis, but have lower metastatic potential. Mechanistically, different oncogenic gains and dosages evolve along distinct evolutionary routes, licensed by defined allelic states and/or combinations of hallmark tumour suppressor alterations (Cdkn2a, Trp53, Tgfβ-pathway). Thus, evolutionary constraints and contingencies direct oncogenic dosage gain and variation along defined routes to drive the early progression of PDAC and shape its downstream biology. Our study uncovers universal principles of Ras-driven oncogenesis that have potential relevance beyond pancreatic cancer.

Copy number variation arising from gene conversion on the human Y chromosome

We describe the variation in copy number of a ~ 10 kb region overlapping the long intergenic noncoding RNA (lincRNA) gene, TTTY22, within the IR3 inverted repeat on the short arm of the human Y chromosome, leading to individuals with 0-3 copies of this region in the general population. Variation of this CNV is common, with 266 individuals having 0 copies, 943 (including the reference sequence) having 1, 23 having 2 copies, and two having 3 copies, and was validated by breakpoint PCR, fibre-FISH, and 10× Genomics Chromium linked-read sequencing in subsets of 1234 individuals from the 1000 Genomes Project. Mapping the changes in copy number to the phylogeny of these Y chromosomes previously established by the Project identified at least 20 mutational events, and investigation of flanking paralogous sequence variants showed that the mutations involved flanking sequences in 18 of these, and could extend over > 30 kb of DNA. While either gene conversion or double crossover between misaligned sister chromatids could formally explain the 0-2 copy events, gene conversion is the more likely mechanism, and these events include the longest non-allelic gene conversion reported thus far. Chromosomes with three copies of this CNV have arisen just once in our data set via another mechanism: duplication of 420 kb that places the third copy 230 kb proximal to the existing proximal copy. Our results establish gene conversion as a previously under-appreciated mechanism of generating copy number changes in humans and reveal the exceptionally large size of the conversion events that can occur.

Investigations on Blending and Foaming Behavior of Styrene-Ethylene-Butylene-Styrene/Polystyrene Blends

The interplay of screw speed and residence time during polymer blend extrusion profoundly influences blend properties. Herein, blends of styrene-ethylene-butylene-styrene (SEBS) and polystyrene (PS) containing 30% by weight PS were prepared at a constant feed rate but different screw speeds (50, 100, 200 and 300 min−1). The blend produced at 100 min−1 (B100) possessed a finer morphology, better mechanical and rheological properties, attributed to suitability of residence time and viscosity ratio. When batch foamed with carbon dioxide at 110°C and 100°C, all blends produced stable foams. B100 foams exhibited higher volume expansion ratio (VE) due to higher complex viscosity and storage modulus. When foaming was conducted at 35°C, all foams shrank. B100 foams possessed higher cell density, lower VE and showed faster shrinkage due to increased nucleation and hindered expansion by the finely dispersed stiff PS aggregates during selective foaming of the elastomeric phase.

A closer look at the in vitro electrochemical characterisation of titanium alloys for biomedical applications using in-situ methods

Titanium (Ti) and its alloys are widely used in several biomedical applications, particularly as permanent orthopaedic implants. Electrochemical testing provides a means to perform accelerated corrosion testing, however whilst results from polarisation testing for Ti and its alloys to date have been generally useful, they are also rather limited on the basis of several reasons. One reason is that the polarisation curves for Ti and its alloys in simulated body fluids all appear rather similar, and they do not present a classical 'breakdown' or pitting potential, making discrimination between alloys difficult. Of practical relevance however, are two key issues; (1) how do Ti alloys respond to a breakdown event? (i.e. do they readily 'repassivate'?), and, (2) what is that actual rate of Ti ion loss from exposure to physiological conditions? The answers to these questions are probed herein. Several Ti alloys of either unique composition or different fabrication method were studied, including commercially pure Ti (cp-Ti), Ti-6Al-4V, Ti-29Nb-13Ta-4.5Zr (TNTZ), selective laser melted Ti-6Al-4V, direct laser deposited cp-Ti, Ti-35Nb-15Zr, and Ti-25Nb-8Zr. Results reveal that both fabrication method and alloying influence 'repassivation' behaviour. Furthermore, atomic emission spectroelectrochemistry as applied to cp-Ti indicated actual dissolution currents of ∼2-3μA/cm^-2 (i.e. ∼9μm/yr) in the range of the corrosion potential, also revealing such dissolution is persistent, even with cathodic polarisation, and definitively revealing that the presence of hydrogen peroxide and albumin activate anodic dissolution of Ti.

STATEMENT OF SIGNIFICANCE

We believe the paper makes a significant and important contribution to the field of permanent implant biomaterials. Whilst we concede that the paper does not include any in vivo work, the timeliness of the work, and the completely new nature of the findings, we believe carries the impact required for Acta Biomaterialia. Key highlights include:All of the above combine to produce a manuscript that we believe has wide appeal, and can be used as both a port of reference to those working with Ti biomaterials, and also those wishing to apply useful characterisation techniques to their own work (with two very novel methods demonstrated herein, along with the unique information they provide).

Interfacial structures and energetics of the strengthening precipitate phase in creep-resistant Mg-Nd-based alloys

The extraordinary creep-resistance of Mg-Nd-based alloys can be correlated to the formation of nanoscale-platelets of β₁-Mg₃Nd precipitates, that grow along 〈110〉_Mg in bulk hcp-Mg and on dislocation lines. The growth kinetics of β₁ is sluggish even at high temperatures, and presumably occurs via vacancy migration. However, the rationale for the high-temperature stability of precipitate-matrix interfaces and observed growth direction is unknown, and may likely be related to the interfacial structure and excess energy. Therefore, we study two interfaces– {112}_β1/{100}_Mg and {111}_β1/{110}_Mg– that are commensurate with β₁/hcp-Mg orientation relationship via first principles calculations. We find that β₁ acquires plate-like morphology to reduce small lattice strain via the formation of energetically favorable {112}_β1/{100}_Mg interfaces, and predict that β₁ grows along 〈110〉_Mg on dislocation lines due to the migration of metastable {111}_β1/{110}_Mg. Furthermore, electronic charge distribution of the two interfaces studied here indicated that interfacial-energy of coherent precipitates is sensitive to the population of distorted lattice sites, and their spatial extent in the vicinity of interfaces. Our results have implications for alloy design as they suggest that formation of β₁-like precipitates in the hcp-Mg matrix will require well-bonded coherent interface along precipitate broad-faces, while simultaneously destabilizing other interfaces.

Development of an E-learning System for the Endoscopic Diagnosis of Early Gastric Cancer: An International Multicenter Randomized Controlled Trial

Background

In many countries, gastric cancer is not diagnosed until an advanced stage. An Internet-based e-learning system to improve the ability of endoscopists to diagnose gastric cancer at an early stage was developed and was evaluated for its effectiveness.

Methods

The study was designed as a randomized controlled trial. After receiving a pre-test, participants were randomly allocated to either an e-learning or non-e-learning group. Only those in the e-learning group gained access to the e-learning system. Two months after the pre-test, both groups received a post-test. The primary endpoint was the difference between the two groups regarding the rate of improvement of their test results.

Findings

515 endoscopists from 35 countries were assessed for eligibility, and 332 were enrolled in the study, with 166 allocated to each group. Of these, 151 participants in the e-learning group and 144 in the non-e-learning group were included in the analysis. The mean improvement rate (standard deviation) in the e-learning and non-e-learning groups was 1·24 (0·26) and 1·00 (0·16), respectively (P < 0·001).

Interpretation

This global study clearly demonstrated the efficacy of an e-learning system to expand knowledge and provide invaluable experience regarding the endoscopic detection of early gastric cancer (R000012039).

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This report establishes that an e-learning system on the Internet can improve the diagnostic ability of endoscopists.

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Countless endoscopists worldwide can access the system to learn how to make an endoscopic diagnosis of early gastric cancer.

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The e-learning system could be modified to provide education regarding endoscopic diagnosis in other organs.

This is the first report to demonstrate how an e-learning system based on the Internet can improve the diagnostic ability of gastrointestinal endoscopists worldwide. There is no limit to the number of endoscopists who can access the system and benefit from this opportunity to learn how to make an endoscopic diagnosis of early gastric cancer. This e-learning system could be modified to provide education regarding endoscopic diagnosis in other organs such as the large intestine and the esophagus, as well as the stomach. It may contribute to human welfare and health by reducing the mortality from gastrointestinal cancer.

Formin Is Associated with Left-Right Asymmetry in the Pond Snail and the Frog

While components of the pathway that establishes left-right asymmetry have been identified in diverse animals, from vertebrates to flies, it is striking that the genes involved in the first symmetry-breaking step remain wholly unknown in the most obviously chiral animals, the gastropod snails. Previously, research on snails was used to show that left-right signaling of Nodal, downstream of symmetry breaking, may be an ancestral feature of the Bilateria [1 and 2]. Here, we report that a disabling mutation in one copy of a tandemly duplicated, diaphanous-related formin is perfectly associated with symmetry breaking in the pond snail. This is supported by the observation that an anti-formin drug treatment converts dextral snail embryos to a sinistral phenocopy, and in frogs, drug inhibition or overexpression by microinjection of formin has a chirality-randomizing effect in early (pre-cilia) embryos. Contrary to expectations based on existing models [3, 4 and 5], we discovered asymmetric gene expression in 2- and 4-cell snail embryos, preceding morphological asymmetry. As the formin-actin filament has been shown to be part of an asymmetry-breaking switch in vitro [6 and 7], together these results are consistent with the view that animals with diverse body plans may derive their asymmetries from the same intracellular chiral elements [8].

Chromosome engineering in zygotes with CRISPR/Cas9

Deletions, duplications, and inversions of large genomic regions covering several genes are an important class of disease causing variants in humans. Modeling these structural variants in mice requires multistep processes in ES cells, which has limited their availability. Mutant mice containing small insertions, deletions, and single nucleotide polymorphisms can be reliably generated using CRISPR/Cas9 directly in mouse zygotes. Large structural variants can be generated using CRISPR/Cas9 in ES cells, but it has not been possible to generate these directly in zygotes. We now demonstrate the direct generation of deletions, duplications and inversions of up to one million base pairs by zygote injection. genesis 54:78–85, 2016. © 2016 The Authors. genesis Published by Wiley Periodicals, Inc.

Evolution of the single-mode Rayleigh-Taylor instability under the influence of time-dependent accelerations

From nonlinear models and direct numerical simulations we report on several findings of relevance to the single-mode Rayleigh-Taylor (RT) instability driven by time-varying acceleration histories. The incompressible, direct numerical simulations (DNSs) were performed in two (2D) and three dimensions (3D), and at a range of density ratios of the fluid combinations (characterized by the Atwood number). We investigated several acceleration histories, including acceleration profiles of the general form g(t)∼t^{n}, with n≥0 and acceleration histories reminiscent of the linear electric motor experiments. For the 2D flow, results from numerical simulations compare well with a 2D potential flow model and solutions to a drag-buoyancy model reported as part of this work. When the simulations are extended to three dimensions, bubble and spike growth rates are in agreement with the so-called level 2 and level 3 models of Mikaelian [K. O. Mikaelian, Phys. Rev. E 79, 065303(R) (2009)10.1103/PhysRevE.79.065303], and with corresponding 3D drag-buoyancy model solutions derived in this article. Our generalization of the RT problem to study variable g(t) affords us the opportunity to investigate the appropriate scaling for bubble and spike amplitudes under these conditions. We consider two candidates, the displacement Z and width s^{2}, but find the appropriate scaling is dependent on the density ratios between the fluids-at low density ratios, bubble and spike amplitudes are explained by both s^{2} and Z, while at large density differences the displacement collapses the spike data. Finally, for all the acceleration profiles studied here, spikes enter a free-fall regime at lower Atwood numbers than predicted by all the models.

Complex Magnetism of Lanthanide Intermetallics and the Role of their Valence Electrons: Ab Initio Theory and Experiment

We explain a profound complexity of magnetic interactions of some technologically relevant gadolinium intermetallics using an ab initio electronic structure theory which includes disordered local moments and strong f-electron correlations. The theory correctly finds GdZn and GdCd to be simple ferromagnets and predicts a remarkably large increase of Curie temperature with a pressure of +1.5 K kbar(-1) for GdCd confirmed by our experimental measurements of +1.6  K kbar(-1). Moreover, we find the origin of a ferromagnetic-antiferromagnetic competition in GdMg manifested by noncollinear, canted magnetic order at low temperatures. Replacing 35% of the Mg atoms with Zn removes this transition, in excellent agreement with long-standing experimental data.