Extended C-band tunable multi-channel InP-based coherent receiver PICs

Fully integrated monolithic, multi-channel InP-based coherent receiver PICs and transceiver modules with extended C-band tunability are described. These PICs operate at 33 and 44 Gbaud per channel under dual polarization (DP) 16-QAM modulation. Fourteen-channel monolithic InP receiver PICs show integration and data rate scaling capability to operate at 44 Gbaud under DP 16-QAM modulation for combined 4.9 Tb/s total capacity. Six channel simultaneous operation of a commercial transceiver module at 33 Gbaud is demonstrated for a variety of modulation formats including DP 16-QAM for >1.2Tbit/s aggregate data capacity.

Spectral dynamics of THz pulses generated by two-color laser filaments in air: the role of Kerr nonlinearities and pump wavelength

We theoretically and numerically study the influence of both instantaneous and Raman-delayed Kerr nonlinearities as well as a long-wavelength pump in the terahertz (THz) emissions produced by two-color femtosecond filaments in air. Although the Raman-delayed nonlinearity induced by air molecules weakens THz generation, four-wave mixing is found to impact the THz spectra accumulated upon propagation via self-, cross-phase modulations and self-steepening. Besides, using the local current theory, we show that the scaling of laser-to-THz conversion efficiency with the fundamental laser wavelength strongly depends on the relative phase between the two colors, the pulse duration and shape, rendering a universal scaling law impossible. Scaling laws in powers of the pump wavelength may only provide a rough estimate of the increase in the THz yield. We confront these results with comprehensive numerical simulations of strongly focused pulses and of filaments propagating over meter-range distances.

Modeling emissions from CAFO poultry farms in Poland and evaluating potential risk to surrounding populations

The world-wide use of concentrated animal feeding operations (CAFOs) for livestock production demands the need to evaluate the potential impact to public health. We estimated the exposure of various airborne pollutants for populations residing in close proximity to 10 poultry CAFOs located in Central Poland. Ammonia (NH3), carbon dioxide (CO2), carbon monoxide (CO), hydrogen sulfide (H2S), methane (CH4), nitrogen dioxide (NO2), nitrous oxide (N2O), sulfur dioxide (SO2), and organic dust were the pollutants of interest for this study. Because no monitoring data were available, we used the steady-state Gaussian dispersion model AERMOD to estimate pollutant concentrations for the exposed population in order to calculate the hazard index (HI) for a combined mixture of chemicals. Our results indicate that while the levels of certain pollutants are expected to exceed background levels commonly found in the environment they did not result in calculated hazard indexes which exceeded unity suggesting low potential for adverse health effects for the surrounding community for the mixture of chemicals. The study was conducted through a cooperation between the Agency for Toxic Substances and Disease Registry (ATSDR) in the USA and the Nofer Institute of Occupational Medicine (NIOM) in Poland.

Abstract P2-04-26: Identifying patient-specific neoepitopes for cell-based and vaccine immunotherapy across breast cancer classifications reveals rarely shared recurrent neoepitopes

Introduction: Targeted therapies for breast cancers such as trastuzumab and everolimus have durable clinical benefits for patients that express the relevant biomarkers (HER2 and mTOR respectively). Triple negative breast cancer patients lack these biomarkers and are left with few options. Recent advances in immunotherapy agents against PD-1/CTLA4 for patients with melanoma have yielded amazing clinical benefits for a subset of patients and may have similar results in breast cancer patients, but again the vast majority of patients still undergo disease progression. We analyzed whole genome sequencing (WGS) and RNA sequencing data from The Cancer Genome Atlas (TCGA) to identify neoepitopes among breast cancer patients that could be used to develop next-generation, patient-specific cancer immunotherapies. Neoepitopes are tumor specific markers that arise from mutations acquired from cancer and may represent a path to targeted therapies even in triple negative breast cancers.

Results: We analyzed 99 breast cancer patients from TCGA, containing a mixture of PR+/HER2+/ER+ and TNBC classifications. These breast cancer patient samples were selected by the availability of whole genome sequencing (WGS) data, RNA-sequencing data as well as clinical outcome data. We identified an average of 680 potential neoepitopes per patient based solely on WGS data. To further refine and select high quality neoepitopes we restricted these neoepitopes based on gene expression yielding an average of 304 expressed neoepitopes per patient. We predicted each patient's HLA typing using only omics data, which we then used to predict HLA-expressed neoepitope binding analysis resulting in an average of 11 high-quality tumor specific neoepitopes per patient. We identified few recurrent neoepitopes that were bound and expressed, indicating the need for a personalized medicine approach.

Conclusions: Within the TCGA dataset, the majority of neoepitopes among patients with breast cancer were unique to each patient. Rarely within subsets of breast cancers such as HER2+, we identify neoepitopes that are shared between patients. For breast cancer patients who do not respond to targeted therapies, high-throughput identification of neoepitopes could serve as the basis for the development of next-generation, patient-specific immunotherapies.

Citation Format: Nguyen A, Sanborn JZ, Vaske CJ, Rabizadeh S, Niazi K, Soon-Shiong P, Benz SC. Identifying patient-specific neoepitopes for cell-based and vaccine immunotherapy across breast cancer classifications reveals rarely shared recurrent neoepitopes [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 P2-04-26.

Anisotropic contrast optical microscope

An optical microscope is described that reveals contrast in the Mueller matrix images of a thin, transparent, or semi-transparent specimen located within an anisotropic object plane (anisotropic filter). The specimen changes the anisotropy of the filter and thereby produces contrast within the Mueller matrix images. Here we use an anisotropic filter composed of a semi-transparent, nanostructured thin film with sub-wavelength thickness placed within the object plane. The sample is illuminated as in common optical microscopy but the light is modulated in its polarization using combinations of linear polarizers and phase plate (compensator) to control and analyze the state of polarization. Direct generalized ellipsometry data analysis approaches permit extraction of fundamental Mueller matrix object plane images dispensing with the need of Fourier expansion methods. Generalized ellipsometry model approaches are used for quantitative image analyses. These images are obtained from sets of multiple images obtained under various polarizer, analyzer, and compensator settings. Up to 16 independent Mueller matrix images can be obtained, while our current setup is limited to 11 images normalized by the unpolarized intensity. We demonstrate the anisotropic contrast optical microscope by measuring lithographically defined micro-patterned anisotropic filters, and we quantify the adsorption of an organic self-assembled monolayer film onto the anisotropic filter. Comparison with an isotropic glass slide demonstrates the image enhancement obtained by our method over microscopy without the use of an anisotropic filter. In our current instrument, we estimate the limit of detection for organic volumetric mass within the object plane of ≈49 fg within ≈7 × 7 μm² object surface area. Compared to a quartz crystal microbalance with dissipation instrumentation, where contemporary limits require a total load of ≈500 pg for detection, the instrumentation demonstrated here improves sensitivity to a total mass required for detection by 4 orders of magnitude. We detail the design and operation principles of the anisotropic contrast optical microscope, and we present further applications to the detection of nanoparticles, to novel approaches for imaging chromatography and to new contrast modalities for observations on living cells.

Antifactor Xa levels vs. activated partial thromboplastin time for monitoring unfractionated heparin. A pilot study

WHAT IS KNOWN AND OBJECTIVES

The two most common methods for monitoring unfractionated heparin (UFH) infusion are the activated partial thromboplastin time (aPTT) and the antifactor Xa heparin assay (anti-Xa). The purpose of this study is to compare the performance of an aPTT protocol vs. an anti-Xa protocol in adult patients as defined by the time to reach therapeutic range, the percentage of time the values were within the goal range and the number of times laboratory monitoring was conducted. We then analysed the discordance between paired values of anti-Xa and aPTT.

METHODS

This was a single-centre prospective cohort pilot study conducted from 1 September 2013 to 31 May 2014.

RESULTS

Eighty-five patients were treated with UFH infusion, aPTT monitoring (n = 48), anti-Xa monitoring (n = 37). The number of times aPTT and anti-Xa values were ordered was (median, IQR) 14 (2-34) vs 7 (2-76); P = 0·23. The time to reach therapeutic range in hours was (mean, SD) 22 (20) aPTT vs 15 (13) anti-Xa; P = 0·08. Therapeutic range (>50-100% of the time) was achieved in only 5 (10%) patients in the aPTT group vs. 21 (57%) in the anti-Xa group; P < 0·01. Supratherapeutic values (>50-100%) were observed in 38 (78%) patients in the aPTT group vs. 14 (38%) in the anti-Xa group; P < 0·01. The discordance between aPTT and anti-Xa was evaluated using 234 paired values from 37 patients. There was discordance between anti-Xa and aPTT values 57% of the time. Two patients had bleeding complications requiring blood transfusion or discontinuation of post-pilot protocol.

WHAT IS NEW AND CONCLUSION

Utilizing an anti-Xa protocol to monitor heparin infusion showed favourable results compared with utilizing an aPTT protocol by maintaining values within the therapeutic goal range. The most common discordant pattern in our study was a disproportionate prolongation of aPTT to anti-Xa values. Patients with discordant values presenting with high aPTT to normal anti-Xa values may have an increased risk of bleeding complications.

Understanding Innovation Engines: Automated Creativity and Improved Stochastic Optimization via Deep Learning

The Achilles Heel of stochastic optimization algorithms is getting trapped on local optima. Novelty Search mitigates this problem by encouraging exploration in all interesting directions by replacing the performance objective with a reward for novel behaviors. This reward for novel behaviors has traditionally required a human-crafted, behavioral distance function. While Novelty Search is a major conceptual breakthrough and outperforms traditional stochastic optimization on certain problems, it is not clear how to apply it to challenging, high-dimensional problems where specifying a useful behavioral distance function is difficult. For example, in the space of images, how do you encourage novelty to produce hawks and heroes instead of endless pixel static? Here we propose a new algorithm, the Innovation Engine, that builds on Novelty Search by replacing the human-crafted behavioral distance with a Deep Neural Network (DNN) that can recognize interesting differences between phenotypes. The key insight is that DNNs can recognize similarities and differences between phenotypes at an abstract level, wherein novelty means interesting novelty. For example, a DNN-based novelty search in the image space does not explore in the low-level pixel space, but instead creates a pressure to create new types of images (e.g., churches, mosques, obelisks, etc.). Here, we describe the long-term vision for the Innovation Engine algorithm, which involves many technical challenges that remain to be solved. We then implement a simplified version of the algorithm that enables us to explore some of the algorithm's key motivations. Our initial results, in the domain of images, suggest that Innovation Engines could ultimately automate the production of endless streams of interesting solutions in any domain: for example, producing intelligent software, robot controllers, optimized physical components, and art.

Overexpression of Fibrinogen-Like Protein 2 Promotes Tolerance in a Fully Mismatched Murine Model of Heart Transplantation

Fibrinogen-like protein 2 (FGL2) is an immunomodulatory protein that is expressed by regulatory T cells (Tregs). The objective of this study was to determine if recombinant FGL2 (rFGL2) treatment or constitutive FGL2 overexpression could promote transplant tolerance in mice. Although rFGL2 treatment prevented rejection of fully mismatched cardiac allografts, all grafts were rejected after stopping treatment. Next, we generated FGL2 transgenic mice (fgl2(Tg) ) that ubiquitously overexpressed FGL2. These mice developed normally and had no evidence of the autoimmune glomerulonephritis seen in fgl2(-/-) mice. Immune characterization showed fgl2(Tg) T cells were hypoproliferative to stimulation with alloantigens or anti-CD3 and anti-CD28 stimulation, and fgl2(Tg) Tregs had increased immunosuppressive activity compared with fgl2(+/+) Tregs. To determine if FGL2 overexpression can promote tolerance, we transplanted fully mismatched cardiac allografts into fgl2(Tg) recipients. Fifty percent of cardiac grafts were accepted indefinitely in fgl2(Tg) recipients without any immunosuppression. Tolerant fgl2(Tg) grafts had increased numbers and proportions of Tregs and tolerant fgl2(Tg) mice had reduced proliferation to donor but not third party antigens. These data show that tolerance in fgl2(Tg) recipients involves changes in Treg and T cell activity that contribute to a higher intragraft Treg-to-T cell ratio and acceptance of fully mismatched allografts.

Evaluation of mobile digital light-emitting diode fluorescence microscopy in Hanoi, Viet Nam

SETTING

Hanoi Lung Hospital, Hanoi, Viet Nam.

OBJECTIVE

To compare the accuracy of CellScopeTB, a manually operated mobile digital fluorescence microscope, with conventional microscopy techniques.

DESIGN

Patients referred for sputum smear microscopy to the Hanoi Lung Hospital from May to September 2013 were included. Ziehl-Neelsen (ZN) smear microscopy, conventional light-emitting diode (LED) fluorescence microscopy (FM), CellScopeTB-based LED FM and Xpert(®) MTB/RIF were performed on sputum samples. The sensitivity and specificity of microscopy techniques were determined in reference to Xpert results, and differences were compared using McNemar's paired test of proportions.

RESULTS

Of 326 patients enrolled, 93 (28.5%) were Xpert-positive for TB. The sensitivity of ZN microscopy, conventional LED FM, and CellScopeTB-based LED FM was respectively 37.6% (95%CI 27.8-48.3), 41.9% (95%CI 31.8-52.6), and 35.5% (95%CI 25.8-46.1). The sensitivity of CellScopeTB was similar to that of conventional LED FM (difference -6.5%, 95%CI -18.2 to 5.3, P = 0.33) and ZN microscopy (difference -2.2%, 95%CI -9.2 to 4.9, P = 0.73). The specificity was >99% for all three techniques.

DISCUSSION

CellScopeTB performed similarly to conventional microscopy techniques in the hands of experienced TB microscopists. However, the sensitivity of all sputum microscopy techniques was low. Options enabled by digital microscopy, such as automated imaging with real-time computerized analysis, should be explored to increase sensitivity.

Bridge to transplantation using paracorporeal biventricular assist devices or the syncardia temporary total artificial heart: is there a difference?

AIM

Biventricular support can be achieved using paracorporeal ventricular assist devices (p-BiVAD) or the Syncardia temporary total artificial heart (t-TAH). The purpose of the present study was to compare survival and morbidity between these devices.

METHODS

Data from 2 French neighboring hospitals were reviewed. Between 1996 and 2009, 148 patients (67 p-BiVADs and 81 t-TAH) underwent primary, planned biventricular support. There were 128 (86%) males aged 44±13 years.

RESULTS

Preoperatively, p-BiVAD recipients had significantly lower systolic and diastolic blood pressures, more severe hepatic cytolysis and higher white blood cell counts than t-TAH recipients. In contrast, t-TAH patients had significantly higher rates of pre-implant ECLS and hemofiltration. Mean support duration was 79±100 days for the p-BiVAD group and 71±92 for t-TAH group (P=0.6). Forty two (63%) p-BiVAD recipients were bridged to transplantation (39, 58%) or recovery (3, 5%), whereas 51 (63%) patients underwent transplantation in the t-TAH group. Death on support was similar between groups (p-BiVAD, 26 (39%); t-TAH, 30 (37%); P=0.87). Survival while on device was not significantly different between patient groups and multivariate analysis showed that only preimplant diastolic blood pressure and alanine amino-transferase levels were significant predictors of death. Post-transplant survival in the p-BiVAD group was 76±7%, 70±8%, and 58±9% at 1, 3, and 5 years after transplantation, respectively, and was similar to that of the t-TAH group (77±6%, 72±6%, and 70±7%, P=0.60).

CONCLUSION

Survival while on support and up to 5 years after heart transplantation was not significantly different in patients supported by p-BiVADs or t-TAH. Multivariate analysis revealed that survival while on transplantation was not affected by the type of device implanted.

Tumor infiltrating lymphocytes (TIL) and prognosis in oral cavity squamous carcinoma: a preliminary study

OBJECTIVES

Tumor infiltrating lymphocytes (TILs) in the microenvironment reflect may tumor biology and predict outcome. We previously demonstrated that infiltrates of CD4, CD8, and FoxP3 positive lymphocytes were associated with HPV-status and survival in oropharyngeal cancers. To determine if TILs were of prognostic importance in oral cancer, TIL levels were evaluated retrospectively in 52 oral cancer patients treated with surgery and correlations with outcome determined.

METHODS

Complete TIL and clinical data were available for 39 patients. Levels of CD4, CD8, FoxP3 (Treg), CD68 and NK cells were assessed by immunohistochemistry in tumor cores on a tissue microarray. Associations with clinical variables, tobacco and alcohol use and histologic features were assessed using Spearman correlation coefficient and the non-parametric Kruskal-Wallis testing. Time-to-event outcomes were determined using univariate and multivariate Cox models. Median follow up was 60 months.

RESULTS

The ratio of CD4/CD8 (p=.01) and CD8 infiltrates (p=.05) were associated with tumor recurrence but not overall survival. Lower CD4 infiltrates were associated with alcohol use (p=.005) and poor tumor differentiation (p=.02). Interestingly, higher levels of CD68+ macrophages were found associated with positive nodes (p=.06) and poorer overall survival (p=.07). Overall and DSS survival were significantly shorter for patients with positive nodes, extracapsular spread, or perineural invasion.

CONCLUSION

Infiltrating immune cell levels in oral cavity cancer appear influenced by health behaviors and tumor characteristics. In contrast to oropharynx cancer, infiltrates of CD68 positive tumor associated macrophages may contribute to metastatic behavior and outcome in advanced oral cavity carcinoma.

Surgical and clinical confirmation of temporal bone CT findings in patients with otosclerosis with failed stapes surgery

BACKGROUND AND PURPOSE

Prior descriptions of imaging after failed stapes procedures for otosclerosis predated currently available CT technology and/or failed to assess commonly used metallic implants. The purpose of this study was to correlate temporal bone CT findings with clinically and intraoperatively determined causes of surgical failure.

MATERIALS AND METHODS

All patients with otosclerosis undergoing stapedectomy between December 1999 and December 2010 were identified from a search of neurotology clinical records. Patients presenting because of failed stapes surgery and having temporal bone CT scans at the time of revision surgery or clinical evaluation were included. Imaging and clinical records were retrospectively evaluated by a medical student, radiology resident, and senior neuroradiologist. Stapes prosthesis complications and relevant anatomic CT findings were correlated to clinical and intraoperative findings.

RESULTS

Twenty-two of 340 patients met inclusion criteria. Temporal bone CT findings were correlated to intraoperative findings in 17 of 22 patients and to clinical findings in 5 of 22 patients. Surgically confirmed abnormalities included 7 of 7 incus erosions, 3 of 6 piston re-sizings, 3 of 5 granulation tissues, 3 of 5 prosthesis disconnections, 3 of 4 obliterative otosclerosis, 2 of 2 oval window dislocations, and 1 labyrinthine ossificans. Clinically confirmed abnormalities included 2 cases each of superior semicircular canal dehiscence, and wrong piston size, and 1 each of piston disconnection, labyrinthine ossificans, and intravestibular footplate.

CONCLUSIONS

CT evaluation in the setting of failed stapes surgery is challenging. Many postoperative complications such as piston migration, incus necrosis, and overt vestibular penetration are well recognized on temporal bone CT. Of particular note, superior semicircular canal dehiscence is an important contraindication to stapes surgery.

Prevalence of renal impairment among osteoporotic women in the USA, NHANES 2005-2008: is treatment with bisphosphonates an option?

Bisphosphonates are the first-line treatment for osteoporotic (OP) women; however, therapy is not recommended in severe renal impairment (RI). This study examined RI prevalence among OP women. Nearly a quarter of women had moderate RI, and 3.59% would not be recommended for bisphosphonates, demonstrating a need for better therapeutic alternatives.

INTRODUCTION

Bisphosphonates are the recommended first-line treatment for postmenopausal women with OP. However, bisphosphonates are cleared through the kidney, and therapy is not recommended in severe RI due to adverse treatment effects observed with intravenous formulations. The objective of this study was to examine the prevalence of RI among women with OP aged ≥50 years in the USA.

METHODS

Women with OP aged ≥50 years were identified using the 2005-2008 National Health and Nutrition Examination Survey (NHANES) data. OP was defined as prior OP diagnosis, previous hip or spine fracture, or measured lumbar spine/femoral neck bone mineral density (BMD) T-score <-2.5. The 2005 Modification of Diet in Renal Disease (MDRD) formula was used to calculate the glomerular filtration rate (GFR). Moderate and severe RI was defined as GFR 30-59 and 15-29 mL/min, respectively. Bisphosphonate therapy was considered not recommended among women with OP if GFR was <35 mL/min.

RESULTS

The prevalence of OP among women in USA aged ≥50 years was 27% (12.7 million). Nearly a quarter of women with OP (23.54 ± 2.02%; 2.9 million) had moderate RI and 1.88 ± 0.28% (230,000) had severe RI. Correspondingly, bisphosphonate therapy would not be recommended for an estimated 439,000 women with OP (3.59 ± 0.73%).

CONCLUSIONS

Nearly a quarter of postmenopausal women with OP have moderate RI, and over 3% would not be recommended for bisphosphonate treatment. These data reveal a need for better therapeutic alternatives that can be used in this patient population.