Utility of long-read sequencing for All of Us

The All of Us (AoU) initiative aims to sequence the genomes of over one million Americans from diverse ethnic backgrounds to improve personalized medical care. In a recent technical pilot, we compare the performance of traditional short-read sequencing with long-read sequencing in a small cohort of samples from the HapMap project and two AoU control samples representing eight datasets. Our analysis reveals substantial differences in the ability of these technologies to accurately sequence complex medically relevant genes, particularly in terms of gene coverage and pathogenic variant identification. We also consider the advantages and challenges of using low coverage sequencing to increase sample numbers in large cohort analysis. Our results show that HiFi reads produce the most accurate results for both small and large variants. Further, we present a cloud-based pipeline to optimize SNV, indel and SV calling at scale for long-reads analysis. These results lead to widespread improvements across AoU.

Multishot tomography for high-resolution in situ subtomogram averaging

Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can be observed within their native context. Unlike single particle acquisition (SPA), cryo-ET can be slow, which may reduce overall project throughput. We here propose a fast, multi-position tomographic acquisition scheme based on beam-tilt corrected beam-shift imaging along the tilt axis, which yields sub-nanometer in situ STA averages.

[Clinical features of children with Cunninghamella spp. infection: a case report and literature review]

We report a case of mucormycosis induced by Cunninghamella spp. infection in a ten-year-old girl with acute lymphoblastic leukemia, who developed fever and respiratory symptoms after chemotherapy and was diagnosed with invasive fungal disease. Peripheral blood DNA sequences were analyzed using metagenomic next-generation sequencing (mNGS), and by comparison with the Pathogens Metagenomics Database (PMDB), we identified Cunninghamella spp. with sequence number 514 as the pathogen. The patient was treated with amphotericin B combined with posaconazole and showed a favorable response. We searched Pubmed, Embase, CNKI, and Wanfang database for reports of cases of Cunninghamella spp. infection in children and retrieved 22 reported cases (including 12 males) with a median age of 13.5 (3-18) years. In these 22 cases, hematological malignancy was the most common underlying condition (19/22), and most of patients experienced an acute onset and rapid progression with respiratory symptoms (14/20) and fever (16/20) as the most common symptoms. CT imaging often showed unilateral lesions with varying imaging findings, including pulmonary nodules or masses, infiltrative changes, and pleural effusion. Definite diagnoses were established in 18 of the cases, and 4 had probable diagnoses; the lungs and skin were the most frequent organs compromised by the infection. A definite diagnosis of Cunninghamella spp. infection still relied on histopathological examination and fungal culture, but the molecular techniques including PCR and mNGS had shown potentials in the diagnosis. Almost all the cases received antifungal treatment after diagnosis (21/22), and 13 patients also underwent surgeries. Death occurred in 9 (42%) of the cases at a median of 19 (4-54) days after onset of the signs or symptoms. The patients receiving antifungal therapy combined with surgery had a high survival rate (9/13, 69%) than those with antifungal therapy alone (3/8, 37%). Invasive fungal disease is a common complication in immunoco-mpromised patients, but Cunninghamella spp. infection is rare and has a high mortality rate. In cases highly suspected of this disease, active diagnosis and early treatment are critical to improve the survival outcomes of the patients.

A 2-year locomotive exploration and scientific investigation of the lunar farside by the Yutu-2 rover

The lunar nearside has been investigated by many uncrewed and crewed missions, but the farside of the Moon remains poorly known. Lunar farside exploration is challenging because maneuvering rovers with efficient locomotion in harsh extraterrestrial environment is necessary to explore geological characteristics of scientific interest. Chang'E-4 mission successfully targeted the Moon's farside and deployed a teleoperated rover (Yutu-2) to explore inside the Von Kármán crater, conveying rich information regarding regolith, craters, and rocks. Here, we report mobile exploration on the lunar farside with Yutu-2 over the initial 2 years. During its journey, Yutu-2 has experienced varying degrees of mild slip and skid, indicating that the terrain is relatively flat at large scales but scattered with local gentle slopes. Cloddy soil sticking on its wheels implies a greater cohesion of the lunar soil than encountered at other lunar landing sites. Further identification results indicate that the regolith resembles dry sand and sandy loam on Earth in bearing properties, demonstrating greater bearing strength than that identified during the Apollo missions. In sharp contrast to the sparsity of rocks along the traverse route, small fresh craters with unilateral moldable ejecta are abundant, and some of them contain high-reflectance materials at the bottom, suggestive of secondary impact events. These findings hint at notable differences in the surface geology between the lunar farside and nearside. Experience gained with Yutu-2 improves the understanding of the farside of the Moon, which, in return, may lead to locomotion with improved efficiency and larger range.

POS0884 THE ENHANCED LIVER FIBROSIS (ELF) SCORE AS A BIOMARKER OF SKIN FIBROSIS IN SYSTEMIC SCLEROSIS

Background:

Serum fibrotic markers for systemic sclerosis (SSc) remain limited. The Enhanced Liver Fibrosis (ELF) score, originally derived and validated in patients with chronic liver disease, is an algorithm combining 3 serum markers, known as procollagen type III amino terminal propeptide (PIIINP), tissue inhibitor of metalloproteinases 1 (TIMP-1), and hyaluronic acid (HA). The combined score was proved to be superior to the single components in reflecting the severity of liver fibrosis. However, the performance of ELF score and its components has not been fully validated in SSc.

Objectives:

To investigate PIIINP, TIMP-1, HA, and the combined algorithm ELF score as fibrotic markers for SSc skin involvement.

Methods:

Eighty SSc patients (44 dcSSc and 36 lcSSc), fulfilling the 2013 ACR/EULAR criteria with the absence of chronic liver diseases, were enrolled. Eighty age- and sex- matched healthy controls were also included. Serum PIIINP and HA levels were quantified by chemiluminescence immunoassay. Serum TIMP-1 levels were determined by enzyme-linked immunosorbent assay. The ELF score was calculated using the formula ELF score= 2.494 + 0.846*ln(HA) + 0.735*ln(PIIINP) + 0.391*ln(TIMP-1). Results were correlated with clinical profiles including modified Rodnan skin score (mRSS) and interstitial lung disease (ILD).

Results:

Compared with healthy controls, patients with SSc showed significantly elevated serum PIIINP (11.2±4.8 vs. 5.73±1.4μg/L, p<0.001), TIMP-I (123.7±78.6 vs. 67.8±26.5 ng/ml, p<0.001), and ELF score (10.5±0.9 vs. 9.7±0.4, P<0.001). Even higher levels of PIIINP, TIMP-1, and ELF score were observed in dcSSc patients, compared with lcSSc patients (p<0.001, p=0.024, p=0.003, respectively). No significant difference was found in the levels of serum HA between patients and controls. Strong correlations were observed between mRSS and ELF score (r=0.54, p<0.001), and between mRSS and PIIINP(r=0.62, p<0.001), whereas only weak correlations could be observed between mRSS and TIMP-1 (r=0.28, p=0.02), and between mRSS and HA (r=0.26, p=0.03). When stratified by ELF score, using cutoffs proposed for liver fibrosis and cirrhosis, SSc patients with ELF<9.8 showed the lowest mRSS on average, while patients with ELF>11.3 showed the highest (p<0.001). When stratified by serum PIIINP levels, using the 25th and 75th percentiles, SSc patients with serum PIIIINP levels<7.8μg/L showed the lowest mRSS on average, while patients with PIIINP>14.0μg/L showed the highest (p<0.001). Neither the ELF score nor its components showed significant difference between patients with and without ILD.

Conclusion:

The ELF score could be used for reflecting the severity of overall skin involvement in SSc, and serum PIIINP also increased in parallel with the increase of mRSS. Longitudinal prospective studies exploring ELF score or serum PIIINP as fibrotic markers and outcome measures of SSc are warranted.

References:

[1]Lichtinghagen R, Pietsch D, Bantel H, et al. The Enhanced Liver Fibrosis (ELF) score: Normal values, influence factors and proposed cut-off values. Journal of Hepatology. 2013; 59: 236-42.

[2]Abignano G, Blagojevic J, Bissell LA, et al. European multicentre study validates enhanced liver fibrosis test as biomarker of fibrosis in systemic sclerosis. Rheumatology. 2019; 58: 254-59.

Figure 1.

Correlations of mRSS with ELF score (A) and serum PIIINP (B) and distribution of mRSS among different ELF (C) and PIIINP (D) ranges.

Acknowledgements:

The authors have no acknowledgements to declare.

Disclosure of Interests:

None declared

POS0869 PREDICTIVE VALUE OF ANTI-INTERFERON-INDUCIBLE PROTEIN 16 ANTIBODIES FOR DIGITAL ULCERS OF SYSTEMIC SCLEROSIS

Background:

Interferon-inducible protein 16 (IFI-16) is constitutively expressed in vascular endothelial cells and can inhibit the proliferation of human endothelial cells and the formation of capillary-like structures in vitro. Anti-IFI-16 antibodies were reported in 21%-29% of patients with systemic sclerosis (SSc) and were associated with digital vascular events in a few retrospective studies.

Objectives:

To evaluate the presence and the clinical implication of anti-IFI-16 antibodies in Chinese SSc cohort, focusing on the associations with vasculopathy indexes, and to investigate the predictive value of anti-IFI-16 antibodies for the development of digital ulcers (DUs) in SSc prospectively.

Methods:

Patients with SSc presenting to our center between July 2018 and September 2018 were prospectively enrolled. Serum from 42 SSc patients and 42 age- and sex-matched healthy controls were analyzed for anti-IFI-16 antibodies by enzyme-linked immunosorbent assay (ELISA), and was considered positive if the optical density (OD) value was above the mean OD of controls plus two standard deviations. Tissue immunofluorescence was used to evaluate the expression of IFI16 in skin biopsy samples obtained from SSc patients and normal controls. At baseline, nailfold video-capillaroscopy was performed to assess nailfold capillary density of SSc patients. Power Doppler ultrasound was used to grade finger pulp blood flow (0-no observed flow; 1-decreased flow; 2-normal flow), and to measure ulnar and radial artery blood flow and resistive index (RI). All patients were followed up for 6 months to see whether they experienced new onset or recurrent DUs. The association of anti-IFI-16 antibodies with DUs was analyzed using logistic regression.

Results:

Of the 42 SSc patients, 8 (19.0%) were positive for anti-IFI-16 antibodies. Immunofluorescence of skin biopsy samples from SSc patients exhibited enhanced staining of IFI-16 in the dermis, and colocalization with endothelial marker CD31. SSc patients who were positive for anti-IFI-16 antibodies showed higher ulnar artery RI at baseline (0.95±0.09 vs. 0.86±0.09, p=0.015), while no significant differences were found for other vascular parameters, nor for clinical or demographic profiles. Within 6-month follow-up, 14 (33.3%) patients experienced new-onset or recurrent DUs. Univariate logistic regression revealed the presence of DUs at enrollment (p=0.009), anti-IFI-16 antibody (p=0.012), finger pulp blood flow (p=0.027), and ulnar artery RI (p=0.008) could be the predictors for the development of DUs. Multivariate analysis further identified DUs at enrollment (odds ratio [OR]: 10.85; 95% confidence interval [CI]: 1.61-73.18; p=0.014) and anti-IFI-16 antibody (OR: 15.00; 95% CI: 1.13-199.18; p=0.040) as independent risk factors. Among patients without DUs at enrollment, new-onset ulcers occurred in 80% (4/5) and 4.5% (1/22) of those with and without anti-IFI-16 antibody, respectively (p=0.001).

Conclusion:

Anti-IFI-16 antibody is associated with vasculopathy in SSc and could be used as a novel biomarker for indicating the development of DUs.

References:

[1]McMahan ZH, Shah AA, Vaidya D, et al. Anti-interferon-inducible protein 16 antibodies associate with digital gangrene in patients with Scleroderma. Arthritis Rheumatol. 2016; 68(5): 1262-71.

[2]McMahan ZH, Cottrell TR, Wigley FM, et al. Autoantigens targeted in scleroderma patients with vascular disease are enriched in endothelial lineage cells. Arthritis Rheumatol. 2016; 68(10): 2540–49.

Figure 1.

Multivariate logistic analysis for new or recurrent digital ulcers.

Acknowledgements:

The authors would like to thank Doctor Yi Cheng for performing Power Doppler ultrasound assessment.

Disclosure of Interests:

None declared

Molecular and heterogeneous water oxidation catalysts: recent progress and joint perspectives

The recent synthetic and mechanistic progress in molecular and heterogeneous water oxidation catalysts highlights the new, overarching strategies for knowledge transfer and unifying design concepts.

ELECTROACUPUNCTURE IMPROVES INSULIN SENSITIVITY IN HIGH-FAT DIET-INDUCED INSULIN RESISTANT RATS BY ACTIVATING SIRT1 AND GLUT4 IN QUADRICEPS FEMORIS

OBJECTIVES

To assess the effects of electroacupuncture (EA) at the Zusanli (ST36), Guanyuan (CV4), Zhongwan (CV12), and Fenglong (ST40) acupoints on sirtuin 1 (SIRT1) and glucose transporter type 4 (GLUT4) expression in high-fat diet (HFD)-induced insulin-resistant (IR) rats.

METHODS

Wistar rats were divided into normal control (NC), HFD, and HFD+EA groups. NC rats were fed a standard chow diet and did not receive EA. After being fed an HFD for eight weeks, rats in the HFD+EA group received EA at 2 Hz five times a week for eight weeks. Rats in the HFD group did not receive EA.

RESULTS

In HFD-induced IR rats, EA inhibited body weight increase and water intake, which were observed in HFD rats. EA had no effect on fasting blood glucose and postprandial blood sugar levels. Intraperitoneal insulin tolerance testing revealed that EA enhanced insulin sensitivity in HFD-induced IR rats. Compared with NC rats, SIRT1 and GLUT4 were downregulated in the quadriceps femoris of HFD-fed rats but were increased after eight weeks of EA stimulation.

CONCLUSIONS

EA enhanced HFD-induced insulin resistance by activating SIRT1 and GLUT4 in the quadriceps femoris. These results provide powerful evidence supporting the beneficial effects of EA on HFD-induced insulin resistance.

Temperature dependence of the(π,0)anomaly in the excitation spectrum of the 2D quantum Heisenberg antiferromagnet

It is well established that in the low-temperature limit, the two-dimensional quantum Heisenberg antiferromagnet on a square lattice (2DQHAFSL) exhibits an anomaly in its spectrum at short-wavelengths on the zone-boundary. In the vicinity of thepoint the pole in the one-magnon response exhibits a downward dispersion, is heavily damped and attenuated, giving way to an isotropic continuum of excitations extending to high energies. The origin of the anomaly and the presence of the continuum are of current theoretical interest, with suggestions focused around the idea that the latter evidences the existence of spinons in a two-dimensional system. Here we present the results of neutron inelastic scattering experiments and Quantum Monte Carlo calculations on the metallo-organic compound Cu(DCOO)D2O (CFTD), an excellent physical realisation of the 2DQHAFSL, designed to investigate how the anomaly atevolves up to finite temperatures. Our data reveal that on warming the anomaly survives the loss of long-range, three-dimensional order, and that it is thus a robust feature of the two-dimensional system. With further increase of temperature the zone-boundary response gradually softens and broadens, washing out theanomaly. This is confirmed by a comparison of our data with the results of finite-temperature Quantum Monte Carlo simulations where the two are found to be in good accord. In the vicinity of the antiferromagnetic zone centre, there was no significant softening of the magnetic excitations over the range of temperatures investigated.

Low expression of miR-1 promotes osteogenic repair of bone marrow mesenchymal stem cells by targeting TLR1

OBJECTIVE

Bone marrow mesenchymal stem cells (BMSCs) promote bone tissue repair. MiR-1 regulates myogenic and osteogenic differentiation of human adipose tissue stem cells. However, miR-1's effect on BMSCs osteogenesis is unclear.

MATERIALS AND METHODS

Rat BMSCs were isolated and divided into control group, miR-1 group, and si-miR-1 group respectively transfected with miR-1 plasmid and miR-1 siRNA followed by analysis of cell proliferation by MTT assay and Caspase 3 activity. The expression of osteogenic genes Runx2 and OPN was measured by Real Time-PCR. Healthy male Sprague-Dawley rats were separated into fracture group, NC group, and si-miR-1 group followed by analysis of bone mineral density, miR-1 level by Real Time-PCR, type I collagen, and BMP-2 by enzyme-linked immunosorbent assay (ELISA), and TLR1 expression by Western blot.

RESULTS

Transfection of miR-1 siRNA into BMSCs significantly downregulated miR-1 expression, promoted BMSCs cell proliferation, inhibited Caspase 3 activity, as well as promoted osteogenic genes Runx2 and OPN expression and decreased TLR1 expression (p<0.05). The upregulation of miR-1 expression significantly reversed the above changes. TLR1 is a target of miR-1. Downregulation of miR-1 expression in BMSCs of fractured rats significantly increased bone density and ALP activity, promoted type I collagen and BMP-2 expression, and decreased TLR1 expression (p<0.05).

CONCLUSIONS

The downregulation of miR-1 promotes BMSCs osteogenic differentiation via targeting TLR1, which promotes osteogenic differentiation and bone healing.

Comparing Arabidopsis receptor kinase and receptor protein-mediated immune signaling reveals BIK1-dependent differences

Pattern recognition receptors (PRRs) sense microbial patterns and activate innate immunity against attempted microbial invasions. The leucine-rich repeat receptor kinases (LRR-RK) FLS2 and EFR, and the LRR receptor protein (LRR-RP) receptors RLP23 and RLP42, respectively, represent prototypical members of these two prominent and closely related PRR families. We conducted a survey of Arabidopsis thaliana immune signaling mediated by these receptors to address the question of commonalities and differences between LRR-RK and LRR-RP signaling. Quantitative differences in timing and amplitude were observed for several early immune responses, with RP-mediated responses typically being slower and more prolonged than those mediated by RKs. Activation of RLP23, but not FLS2, induced the production of camalexin. Transcriptomic analysis revealed that RLP23-regulated genes represent only a fraction of those genes differentially expressed upon FLS2 activation. Several positive and negative regulators of FLS2-signaling play similar roles in RLP23 signaling. Intriguingly, the cytoplasmic receptor kinase BIK1, a positive regulator of RK signaling, acts as a negative regulator of RP-type immune receptors in a manner dependent on BIK1 kinase activity. Our study unveiled unexpected differences in two closely related receptor systems and reports a new negative role of BIK1 in plant immunity.

[Efficacy of anti-CD19 CAR-T cell therapy in 10 refractory recurrent B cell malignancies]

目的

探讨抗CD19 CAR-T细胞治疗难治复发B细胞肿瘤的疗效和不良反应。

方法

2015年12月至2017年7月北京大学第三医院血液科收治的10例患者，包括难治复发的急性B淋巴细胞白血病（B-ALL）6例，难治复发的B细胞非霍奇金淋巴瘤（NHL）4例，采用抗CD19 CAR-T细胞治疗后观察治疗效果及不良反应。

结果

输注后第28天进行近期疗效评估，其中6例ALL患者4例（66.7%）完全缓解（CR），1例（16.7%）部分缓解（PR）；总反应率（ORR）为83.3%。3例弥漫大B细胞淋巴瘤（DLBCL）患者1例达CR。1例套细胞淋巴瘤（MCL）患者大部分病灶消失，亦有顽固病灶呈进展状态。10例患者均发生细胞因子释放综合征（CRS），主要表现为发热；其中1例患者出现中枢神经系统症状，1例患者出现多脏器功能衰竭，经治疗不良反应均治愈。

结论

抗CD19 CAR-T细胞治疗难治复发B细胞血液系统肿瘤有效，不良反应可控。

Strain-engineering Mott-insulating La2CuO4

The transition temperature T_c of unconventional superconductivity is often tunable. For a monolayer of FeSe, for example, the sweet spot is uniquely bound to titanium-oxide substrates. By contrast for La_2-xSr_xCuO₄ thin films, such substrates are sub-optimal and the highest T_c is instead obtained using LaSrAlO₄. An outstanding challenge is thus to understand the optimal conditions for superconductivity in thin films: which microscopic parameters drive the change in T_c and how can we tune them? Here we demonstrate, by a combination of x-ray absorption and resonant inelastic x-ray scattering spectroscopy, how the Coulomb and magnetic-exchange interaction of La₂CuO₄ thin films can be enhanced by compressive strain. Our experiments and theoretical calculations establish that the substrate producing the largest T_c under doping also generates the largest nearest neighbour hopping integral, Coulomb and magnetic-exchange interaction. We hence suggest optimising the parent Mott state as a strategy for enhancing the superconducting transition temperature in cuprates.

Hartmann characterization of the PEEM-3 aberration-corrected X-ray photoemission electron microscope

Aberration correction by an electron mirror dramatically improves the spatial resolution and transmission of photoemission electron microscopes. We will review the performance of the recently installed aberration corrector of the X-ray Photoemission Electron Microscope PEEM-3 and show a large improvement in the efficiency of the electron optics. Hartmann testing is introduced as a quantitative method to measure the geometrical aberrations of a cathode lens electron microscope. We find that aberration correction leads to an order of magnitude reduction of the spherical aberrations, suggesting that a spatial resolution of below 100 nm is possible at 100% transmission of the optics when using x-rays. We demonstrate this improved performance by imaging test patterns employing element and magnetic contrast.

Transmission electron microscopy as an important tool for characterization of zeolite structures

This review presents various TEM techniques including electron diffraction, high-resolution TEM and scanning TEM imaging, and electron tomography and their applications for structure characterization of zeolite materials.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm3, i.e. no more than 6 × 105 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

[Analysis of survival and treatment outcome of young patients with high-risk diffuse large B cell lymphoma]

Objective: To analyze clinical feature and treatment outcome of young patients with high-risk diffuse large B cell lymphoma. Methods: A total of 122 young patients with high-risk diffuse large B cell lymphoma who were treated in Third Hospital of Peking University during the period from January 2000 to April 2015 were retrospectively analyzed, and the clinical features, laboratory data were included in Kaplan-Meier and prognostic analysis. Results: In our center, the incidence of young high-risk DLBCL was 27.1% in all DLBCL patients, median age was 44.0 years, 99.2% patients belong to Ⅲ and Ⅳstage, 50% patients had more than two extranodal organs involvement, and the higher proliferation index(Ki-67≥80%) was present in 63.1% of patients, Immunohistochemistry showed that 36.7% patients in 30 cases were double-expressed DLBCL. The overall response rate(ORR) for the whole group was 79.4%, the complete response rate was 39.7% , the 3, 5-year progression free survival rate was 59.8% and 57.0%, the 3, 5-year overall survival rate was 63.5% and 57.8%, respectively. 44.3% patients were refractory-relapsed DLBCL. Rituximab can improve the survival of patients and 3-year overall survival rate was 75.2% vs 46.1%(P=0.001). High-dose chemotherapy was superior to CHOP regimen which 3-year overall survival rate was 84.6% vs 54.1%(P=0.006). Compared with chemotherapy group , auto-hematopoietic stem cell transplantation can improve prognosis of patients and 3-year overall survival rate was 93.4% vs 48.3%(P<0.001). The level of Ki-67, B symptom, ECOG score, the level of LDH, WBC and albumin, ESR level, anemia, rituximab therapy, initial regimens, ASCT, initial treatment outcome and refractory-relapsed were predictive of overall survival. Multivariate analysis indicated that albumin level(RR=5.462, P=0.019), initial treatment outcome(RR=34.863, P<0.001) and refractory-relapsed (RR=24.374, P<0.001)were independent prognostic risk factors. Conclusions: Young patients with high-risk DLBCL were highly aggressive in clinical and pathological features . Rituximab and high-dose regimens can improve the survival of patients.

Abstract P2-10-04: Using the 21-gene assay from core needle biopsies to choose neoadjuvant therapy for breast cancer: A multi-center trial

Neoadjuvant systemic therapy (NST) can facilitate breast conserving surgery (BCS) for large cancers. While hormone receptor positive (HR+) cancers respond to neoadjuvant chemotherapy (NCT), pathologic complete responses (pCR) are unlikely. Neoadjuvant hormonal therapy (NHT) may make BCS possible with less toxicity than NCT. We hypothesized that the Oncotype Dx® 21-gene Recurrence Score (RS), could guide the decision to treat with NHT versus NCT to facilitate BCS. This hypothesis is based on the ability of the RS to identify ER+ patients (pts) likely to benefit from adjuvant CT vs unlikely to benefit, as well as prior studies showing that pts with a low RS have no pCRs when receiving NCT (Yardley, et al 2015).

Methods: This prospective multi-center study enrolled pts with HR+, HER2-negative, invasive breast cancers not suitable for BCS (size ≥ 2 cm). Diagnosis was made by core needle biopsy (bx). Tissue blocks from the bx's were sent to Genomic Health for RS testing. Pts whose tumors had a RS &lt; 11 were to receive NHT; pts with RS &gt;25 tumors were to receive NCT; pts with midrange RS of 11-25 were randomized to NHT or NCT.

The primary objective was the feasibility of randomizing pts with RS values 11-25 between NHT and NCT. The primary endpoint was whether 1/3 or more of randomized pts would refuse assigned treatment. Secondary endpoints included: clinical partial and complete response (cPR, cCR) rates, overall clinical response rates (CR), pCR in the breast, pCR in the breast and nodes and successful BCS. One-sample binomial test was used to compare the observed refusal rate with 1/3, along with its 95% CI. Fisher's exact test, logistic regression (for a binary endpoint), and/or ordinal regression (for an ordinal endpoint) were used to compare the 4 treatment groups for secondary endpoints.

Results: Seven US and Canadian centers enrolled 64 pts; 5 were excluded (1 delay in RS result, 1 lost block, 1 HR testing discrepancy, 2 not eligible). Of 33 pts with RS 11-25, 5 (15%; 95% CI =2.9% - 27.4%) refused assignment to NCT (2 chose NHT and finished the study). This was significantly lower than the 33% target (binomial test, p=0.0292). Results for other endpoints are shown in the Table (according to treatment received); the total number of pts for the analyses is 55; 1 pt had missing data for clinical response.

Results According to TreatmentTreatment GroupRS&lt;11 NHTRS 11-25 NHTRS 11-25 NCTRS&gt;25 NCTOverall PNN=12N=18N=11N=14 cCR8.3%22.2%36.4%28.6%0.0422cPR75%27.8%36.4%64.3% CR (cCR + cPR)83.3%50%72.7%92.9%0.0490pCR Breast8.3%6%021.4%NSpCR Breast + Nodes00014.3%NSSuccessful BCS75%72.2%63.6%57.1%NS

Conclusions:This pilot showed the feasibility of using the RS to guide NST, with only a 15% refusal rate of randomly assigned treatment. Of greater interest is the finding that pts with a RS &lt;11 had a high CR rate with NHT and that pts with a RS 11-25 who received NHT had a similar rate of BCS success as the pts with RS &lt;11. Conversely, pts with RS&gt;25 treated with NCT had the highest CR (cCR + pCR) and pCR rates. These results demonstrate that conducting a similarly designed larger trial is feasible and suggests that for pts with a low RS, NHT is a potentially effective strategy.

Citation Format: Bear HD, Wan W, Robidoux A, Rubin P, Limentani S, White, Jr. RL, Granfortuna J, Hopkins JO, Oldham D, Rodriguez A, Sing AP. Using the 21-gene assay from core needle biopsies to choose neoadjuvant therapy for breast cancer: A multi-center trial [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-10-04.

The versatility and paradox of GDF 11

In addition to its roles in embryonic development, Growth and Differentiation Factor 11 (GDF 11) has recently drawn much interest about its roles in other processes, such as aging. GDF 11 has been shown to play pivotal roles in the rescue of the proliferative and regenerative capabilities of skeletal muscle, neural stem cells and cardiomyocytes. We would be remiss not to point that some controversy exists regarding the role of GDF 11 in biological processes and whether it will serve as a therapeutic agent. The latest studies have shown that the level of circulating GDF 11 correlates with the outcomes of patients with cardiovascular diseases, cancer and uremia. Based on these studies, GDF 11 is a promising candidate to serve as a novel biomarker of diseases. This brief review gives a detailed and concise view of the regulation and functions of GDF 11 and its roles in development, neurogenesis and erythropoiesis as well as the prospect of using this protein as an indicator of cardiac health and aging.

Frontiers of water oxidation: the quest for true catalysts

Development of advanced analytical techniques is essential for the identification of water oxidation catalysts together with mechanistic studies.

Cryo-Electron Tomography and Subtomogram Averaging

Cryo-electron tomography (cryo-ET) allows 3D volumes to be reconstructed from a set of 2D projection images of a tilted biological sample. It allows densities to be resolved in 3D that would otherwise overlap in 2D projection images. Cryo-ET can be applied to resolve structural features in complex native environments, such as within the cell. Analogous to single-particle reconstruction in cryo-electron microscopy, structures present in multiple copies within tomograms can be extracted, aligned, and averaged, thus increasing the signal-to-noise ratio and resolution. This reconstruction approach, termed subtomogram averaging, can be used to determine protein structures in situ. It can also be applied to facilitate more conventional 2D image analysis approaches. In this chapter, we provide an introduction to cryo-ET and subtomogram averaging. We describe the overall workflow, including tomographic data collection, preprocessing, tomogram reconstruction, subtomogram alignment and averaging, classification, and postprocessing. We consider theoretical issues and practical considerations for each step in the workflow, along with descriptions of recent methodological advances and remaining limitations.

Exploring structural phase transitions of ion crystals

Phase transitions have been a research focus in many-body physics over past decades. Cold ions, under strong Coulomb repulsion, provide a repealing paradigm of exploring phase transitions in stable confinement by electromagnetic field. We demonstrate various conformations of up to sixteen laser-cooled (40)Ca(+) ion crystals in a home-built surface-electrode trap, where besides the usually mentioned structural phase transition from the linear to the zigzag, two additional phase transitions to more complicated two-dimensional configurations are identified. The experimental observation agrees well with the numerical simulation. Heating due to micromotion of the ions is analysed by comparison of the numerical simulation with the experimental observation. Our investigation implies very rich and complicated many-body behaviour in the trapped-ion systems and provides effective mechanism for further exploring quantum phase transitions and quantum information processing with ultracold trapped ions.

Design of in-flight fragment separator using high-power primary beams in the energy of a few hundred MeV/u

An in-flight fragment separator usually requires large acceptance and high momentum resolution to minimize the loss of a rare isotope beam of interest produced at a thin target, which is especially important when (238)U fission reactions in the energy of 200 MeV/u are used. The production target and beam dump are located in the pre-separator, where a beam power of up to 400 kW is dissipated. The area is surrounded by thick radiation shielding walls, which result in long drift spaces between adjacent magnetic components at various locations and an asymmetrical layout. Efforts have been made to minimize non-linear effects in the pre-separator beam optics with trials of different separator configurations and correction schemes using COSY Infinity and GICOSY. The main separator is configured to be mirror symmetric such that correction with hexapole and octupole coils can be more readily applied. The separator configuration was finalized to allow the facility design to proceed and the key components including superconducting magnets have been designed and prototyped. In addition, the separator design has been evaluated using LISE++ including a set of wedge degraders at dispersive focal planes to improve the yield and purity of selected isotope beam.

Polymorphisms of uric transporter proteins in the pathogenesis of gout in a Chinese Han population

In this study, we analyzed single nucleotide polymorphisms (SNP) in urate transporter genes to examine the pathogenesis of gout. We conducted a 1:1-matched case-control study that included 110 patients with acute gout attacks as the patient group and 110 healthy age- and gender-matched subjects as the control group. Clinical parameters were recorded and blood biochemistry tests were conducted for both groups. Multivariate logistic regression analysis was used to analyze the data. Hyperuricemia, hypercholesterolemia, and hypertriglyceridemia were found to be the main risk factors for the onset of gout, with relative risks of 29.2 (P < 0.001), 25.5 (P = 0.003), and 11.2 (P < 0.001). For all detected SNP, rs2231142, located in ABCG2, showed the largest frequency differences for the G/G, G/T, and T/T genotypes between groups: the distribution of these genotypes in the case group was 22, 49, and 26 individuals, respectively, and was 54, 38, and 9 individuals, respectively, in the control group. There was a statistically significant difference between the 2 groups (P < 0.001) and the odds ratio was 7.091 (95% confidence interval = 2.867-17.541). Other SNPs (rs1165196, rs1165205, rs1183201, rs17300741, rs2078267, rs2242206, rs3733591, and rs9358856) showed no significant difference between the groups (P > 0.05). The risk factors of gout were hyperuricemia, hypercholesterolemia, hypertriglyceridemia, and the T/T genotype of the rs2231142 locus in the ABCG2 gene; expression of the G/G genotype may be a protective factor against gout development.

Restoring defect structures in 3C-SiC/Si (001) from spherical aberration-corrected high-resolution transmission electron microscope images by means of deconvolution processing

The [110] cross-sectional samples of 3C-SiC/Si (001) were observed with a spherical aberration-corrected 300 kV high-resolution transmission electron microscope. Two images taken not close to the Scherzer focus condition and not representing the projected structures intuitively were utilized for performing the deconvolution. The principle and procedure of image deconvolution and atomic sort recognition are summarized. The defect structure restoration together with the recognition of Si and C atoms from the experimental images has been illustrated. The structure maps of an intrinsic stacking fault in the area of SiC, and of Lomer and 60° shuffle dislocations at the interface have been obtained at atomic level.

A novel system for measurement of the transverse electron momentum distribution from photocathodes

The transverse momentum of electrons produced by a photocathode contributes significantly to the performance of several different types of accelerator-based light sources, such as Free Electron Lasers, as well as systems designed for ultrafast electron diffraction and dynamic transmission electron microscopy. Minimization of the transverse emittance from photocathodes is the subject of intensive research, and therefore measurement of this parameter is of great importance. Here, we describe a simple system that offers real time measurements of transverse emittance and can be easily integrated into the photocathode fabrication process.

Mussel-inspired nanofibrous sheet for suture-less stomach incision surgery

We report a dopamine-based crosslinker-conjugated gelatin/polycaprolactone nanofibrous sheet. The nanosheet was then employed to treat stomach incisions without sutures during surgery.

Abstract P1-01-17: Sentinel node biopsy for breast cancer: Intraoperative injection of radiocolloid

INTRODUCTION. Preoperative injection of radiocolloid for axillary sentinel node biopsy for breast cancer is visibly uncomfortable for many patients. We sought to determine whether injection of the radiocolloid once the patient has been anesthetized would be reliable for sentinel lymph node identification when compared to preoperative injection.

METHODS. A cohort of patients with breast cancer who underwent intraoperative injection of radiocolloid was compared to those who received their injection preoperatively. All injections employed 1mCi 0.5 ml of filtered (0.22 micron) Tc-99m sulfur colloid. All operative surgeons directed injections into the retroareolar tissue; some also intradermally directly over the tumor.

RESULTS. 904 sentinel node biopsy procedures were performed in the six years study period. 759 sentinel node biopsies were analyzed, 664 with preoperative injection of radiocolloid for localization and ninety-five with intraoperative injection. The average age of the patients was 56.8 years: 57.3 years in the preoperative injection group and 53.8 years in the intraoperative injection group. 753 of the 759 patients were women.

Sentinel Node Identification. The overall sentinel lymph node identification rate was similar for the two groups: 94.1% for the preoperative injection group and 93.5% for the intraoperative injection group (P = NS). The identification rate remained equivalent for both groups when analyzed by T stage of the tumor. Similarly, the average number of lymph nodes removed did not differ between preoperative vs. intraoperative injection: 2.66 nodes and 2.55 nodes, respectively.

Sentinel Node Positivity. The overall rate of positive sentinel nodes was also similar for the two groups, 24.7% for the preoperative injection group and 26.4% for the intraoperative injection group (P = NS). When analyzed by T stage, the positivity rate remained similar and not statistically significant. T1 tumors were 21.6% positive in the preoperative group versus 23.9% in the intraoperative group, and T2 tumors were 40.1% vs. 37.0%, respectively.

DISCUSSIONS. Our sentinel lymph node identification rate of 93.5% for the intraoperative injection group appears similar to that of the published literature (96-100%). Our study also showed no statistical difference in positive sentinel node biopsy between preoperative injection (24.7%) and intraoperative injection (26.2%) and is comparable to that of others When analyzed by T stage, our study had 23.9% positive sentinel node biopsies for T1, and 37% for T2 with intraoperative injection.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-01-17.

Surface-plasmon resonance-enhanced multiphoton emission of high-brightness electron beams from a nanostructured copper cathode

We experimentally investigate surface-plasmon assisted photoemission to enhance the efficiency of metallic photocathodes for high-brightness electron sources. A nanohole array-based copper surface was designed to exhibit a plasmonic response at 800 nm, fabricated using the focused ion beam milling technique, optically characterized and tested as a photocathode in a high power radio frequency photoinjector. Because of the larger absorption and localization of the optical field intensity, the charge yield observed under ultrashort laser pulse illumination is increased by more than 100 times compared to a flat surface. We also present the first beam characterization results (intrinsic emittance and bunch length) from a nanostructured photocathode.

Erdheim-Chester disease in a child

Erdheim-Chester disease (ECD) is a rare systemic non-Langerhans histiocytosis that affects multiple organ systems. It occurs more often in adults, and paediatric ECD is extremely rare. The diagnosis of ECD can be established based on clinical presentations and imaging but the final diagnosis should be based on biopsy. Treatment of ECD has involved the use of corticosteroids, radiotherapy, chemotherapy, surgery and haematopoietic stem cell transplantation, yet the efficacy of these treatments is difficult to determine. At present, it is thought that the treatment of interferon-alpha (IFN-alpha) is safe and effective for ECD. Herein, we report on an 11-year old girl who was admitted to hospital because of systemic bone pain and limping, and the final diagnosis of ECD was based on evidence provided by her clinical presentation, imaging and biopsy of a lesion of the right ilium. The patient was treated with subcutaneous IFN-alpha at a dosage of 3 x 10(6) units three times weekly for 19 months. We thought that the treatment of IFN-alpha was safe and effective for the girl's clinical manifestations, and IFN-alpha might be a valuable first-line therapy for paediatric ECD.