Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA

Background: Cancer cells may undergo mutations beyond their original causal changes, resulting in clonal expansion, and potentially driving tumor heterogeneity and evolution. Our hypothesis was that additional, "third hit" genetic changes in clonally derived tumors, originally generated by the same oncogenic stimulus, would have different phenotypes.

Methods: Epithelial cells were isolated from LSL-KrasG12D+/-/Trp53fl/fl/Rosa-CAG-LSL-tdTomato+/- and C57BL/6 control mouse tracheas and were cultured on plastic. On day 3, cells were treated with an adenovirus expressing Cre recombinase. After 7 days, single EPCAM+, 7-aminoactinomycin D (7-AAD)-, and tdTomato+ cells from the LSL-KrasG12D+/-/Trp53fl/fl/Rosa-CAG-LSL-tdTomato+/- mouse, and EPCAM+/ 7-AAD- cells from the control mouse were FACS sorted, and individually seeded in 96-well plates. Clones developing in each well were passaged separately and characterized using growth curves on plastic, staining for lineage markers, and colony forming efficiency (CFE) and colony morphology in 3D culture. Selected clones were further investigated in vivo after subcutaneous injection into the flanks of NOD/SCID mice. Agilent SureSelect targeted exome sequencing was used to evaluate genetic variations in cells derived from each cell clone.

Results: Thirty-five LSL-KrasG12D+/-/Trp53fl/fl/Rosa-CAG-LSL-tdTomato+/- transformed clones and 2 control mouse clones were serially passaged, and 4 transformed cell lines representing distinct phenotypes (named MT1, 2, 3, and 4), were identified based on growth rates, lineage marker staining, CFE, and 3D colony morphology. All 4 clones were pancytokeratin+, 3 were thyroid trasnscription factor-1 (TTF-1)+ and one was p63+. All 4 cell lines generated tumors in NOD/SCID mice, which exhibited variable histology and marker expression. Exome sequencing revealed unique copy number profiles. Specifically, MT1 had gains and losses in chromosome 3, MT2 had losses in chromosome 9, MT3 had losses in chromosomes 7 and 14, and MT4 had losses in chromosome 7. Mutations potentially representing third hits were identified in each cell line, particularly Ss18l1 (synovial sarcoma translocation gene on chromosome 18-like 1) and Gas7 (growth arrest specific 7) in MT1, Runx1 (runt related transcription factor 1) and Dicer1 (dicer 1, ribonuclease type III) in MT2, Apc (adenomatous polyposis coli) in MT3, and Csmd1 (CUB and Sushi multiple domains 1) in MT4.

Conclusions: Multiple single cell derived mouse tracheal epithelial tumor cell clones were generated from a single LSL-KrasG12D+/-/Trp53fl/fl/Rosa-CAG-LSL-tdTomato+/- mouse. Selected clones exhibited unique growth rates, lineage marker expression patterns, CFE, 3D cell morphology and variable in vivo tumor histology and marker expression. Unique copy number aberrations and third hit mutations likely generate distinct clone phenotypes, driving tumor heterogeneity and evolution.

Citation Format: Sang-Won Um, Ping-Jie Xiao, David Neil Hayes, William Y. Kim, Scott H. Randell. Third hit genetic changes and clonal heterogeneity in a genetically engineered mouse lung cancer model. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 62. doi:10.1158/1538-7445.AM2014-62


This work examines a data-intensive irregular application from genomics that represents a type of Generalized N-Body problems, one of the "seven giants" of the NRC Big Data motifs. In this problem, computations (genome alignments) are performed on sparse data-dependent pairs of inputs, with variable cost computation and variable datum sizes. Unlike simulation-based N-Body problems, there is no inherent locality in the pairwise interactions, and the interaction sparsity depends on particular parameters of the input, which can also affect the quality of the output. We build-on a pre-existing bulk-synchronous implementation, using collective communication in MPI, and implement a new asynchronous one, using cross-node RPCs in UPC++. We establish the intranode comparability and efficiency of both, scaling from one to all core(s) on node. Then we evaluate the multinode scalability from 1 node to 512 nodes (32,768 cores) of NERSC's Cray XC40 with Intel Xeon Phi "Knight's Landing" nodes. With real workloads, we examine the load balance of the irregular computation and communication, and the costs of many small asynchronous messages versus few large-aggregated messages, in both latency and overall application memory footprint. While both implementations demonstrate good scaling, the study reveals some of the programming and architectural challenges for scaling this type of data-intensive irregular application, and contributes code that can be used in genomics pipelines or in benchmarking for data analytics more broadly.


Alterations in protein (e.g., biomarkers) expression levels have a significant correlation with tumor development and prognosis; therefore, it is desired to develop precise methods to differentiate the expression level of proteins in tumor cell lines, especially at the single-cell level. Here, we report a precise and versatile approach of quantifying the protein expression levels of three tumor cell lines in situ using a peptide–Au cluster probe. The probe (Au5Peptide3) consists of a peptide with a specific cell membrane epidermal growth factor receptor (EGFR) targeting ability and an Au cluster for both cell membrane EGFR imaging using confocal microscopy and cell membrane EGFR counting by laser ablation inductively coupled plasma mass spectrometry. Utilizing the peptide–Au cluster probe, we successfully quantify the EGFR expression levels of SMMC-7721, KB, and HeLa cells at a single-cell level and differentiate the EGFR expression levels among these cell lines. The peptide–Au cluster probe, with the ability to differentiate the protein expression level of different cell lines, shows exceptional promise for providing reliable predictive and prognostic information of tumors at a single-cell level.

acs-specific: authorchoice/editors choice usage agreement


Ultra-wideband impulse radio (UWB-IR) sensor network has intensive military and commercial applications. However, the interference between UWB and other existed networks should be casually investigated. In this paper, we consider interference mitigation in UWB sensors in the context of cognitive radio (CR). Firstly, we suggest a general state transition model to characterize the working states evolution of legal networks, also referred to as primary users (PU). Spectrum sensing, used to identify the state of PU, is formulated as detection of a corresponding state sequence. Maximum posterior probability (MAP) criterion is adopted to perform spectrum sensing. By exploring potential gain of state transitions, detection probability for nearby networks is improved significantly. Subsequently, based on the radius basis function neural network (RBF), we present a novel spectrum sculptor to design UWB waveforms. Attributed to the excellent reconfiguration of RBF, our scheme can produce UWB waveforms tracing available spectrums. The designed waveforms can entirely utilize multiple unoccupied bands to maintain uninterrupted communications. Also, sufficient spectral attenuation can be generated in specific bands to mitigate mutual interference between UWB sensors and other networks. Besides, orthogonal waveforms can be easily derived, which either improves transmission performance or provides a flexible accessing strategy for UWB sensors.


The energy demand of China is gradually increasing with the rapid economic development, according to the new low-carbon energy development strategy, China will enhance the renewable energy proportion and reduce the fossil energy, the energy demand forecasting has the important significance for the future energy development planning of China. This study built an energy forecasting model based on the Long-Range Energy Alternatives Planning (LEAP) computer software in order to analyze the future energy development of China. The LEAP model was used to estimate the total energy demand, electricity demand and the energy demand structure by 2030 of four sectors of industries in BAU, BAL and BAH three different scenarios. As the forecasting results shown, the energy demand will reach 4,800-5100 Mtce in 2020 and 5,300-5,700 Mtce in 2030, and although the coal will dominate the energy, it will peak by 2030, the renewable energy will enhance its proportion in the energy structure, especially the wind and solar energy. The electricity will increasing stably increase near 10,000 Billion kWh by 2030. The prime objective was to give some reference of the long-term energy development planning policy, which help reducing the carbon emissions and air pollution to the environment.


Purpose – The purpose of this paper is to determine the relationship between the number of waves a surfer will catch, the surfer's characteristics, and the surf conditions; and utilize this relationship to explain wave allocation strategies chosen by surfers. Design/methodology/approach – The study employed a discrete event simulation to model surfers at a well-known surf break in Southern California. Several experimental designs were implemented in the simulation to measure the effect of a surfer's characteristics and surf conditions on waves caught; and compare different wave allocation strategies. Findings – The number of waves that a surfer will catch is largely dependent upon the surfer's skill level and the wave allocation strategy used at the surf break. Common wave allocation strategies fail with large crowds. Originality/value – This study is the first to model the entire lineup at a surf break, providing quantitative insights into why surfers choose different wave allocation strategies.


During shearing in geological environments, frictional processes, including the wear of sliding rock surfaces, control the nature of the slip events. Multiple studies focusing on natural samples have investigated the frictional behaviour of a large suite of geological materials. However, due to the varied and heterogeneous nature of geomaterials, the individual controls of material properties on friction and wear remain unconstrained. Here, we use variably porous synthetic glass samples (8, 19 and 30% porosity) to explore the frictional behaviour and development of wear in geomaterials at low normal stresses (≤1 MPa). We propose that porosity provides an inherent roughness to material which wear and abrasion cannot smooth, allowing material at the pore margins to interact with the slip surface. This results in an increase in measured friction coefficient from <0.4 for 8% porosity, to <0.55 for 19% porosity and 0.6–0.8 for 30% porosity for the slip rates evaluated. For a given porosity, wear rate reduces with slip rate due to less asperity interaction time. At higher slip rates, samples also exhibit slip weakening behaviour, either due to evolution of the slipping zone or by the activation of temperature-dependent microphysical processes. However, heating rate and peak temperature may be reduced by rapid wear rates as frictional heating and wear compete. The higher wear rates and reduced heating rates of porous rocks during slip may delay the onset of thermally triggered dynamic weakening mechanisms such as flash heating, frictional melting and thermal pressurisation. Hence porosity, and the resultant friction coefficient, work, heating rate and wear rate, of materials can influence the dynamics of slip during such events as shallow crustal faulting or mass movements.


A 32cm long sediment-core was sampled from Kechou reservoir located in Karst area of central Guizhou Province. According to study on grain size pattern and 137Cs dating in the profile, comparing with precipitation records, we determined the sediment ages in different depth of this core. Using the cumulative mass depth, we also calculated the deposit rates in different stages from 1960 to 2004. We improved the traditional 137Cs dating method which only relied on the position of peaks in profile. By analyzing the 137Cs depositing transportation and sedimentation, we found that the absolute values of 137Cs in the certain small catchment often appear in the low level. We believe that the soil erosion, which was caused by precipitation and other reasons, should intensively affect the amount of 137Cs depositing from soil to the sediment in reservoir. That should be the main reason of different pattern of 137Cs distributions in the sediment-core.


BACKGROUND Seborrheic keratosis (SK) is a common benign skin tumor, yet no topical treatments are approved in the United States. OBJECTIVE To evaluate the proprietary, stabilized, high-concentration hydrogen peroxide–based topical solution A-101 (32.5% and 40% concentrations) for treatment of facial SK lesions. MATERIALS AND METHODS In this multicenter, double-blind, vehicle-controlled study, eligible subjects were randomly assigned to receive up to 2 treatments of A-101 40%, A-101 32.5%, or vehicle solution applied to a single facial SK lesion. The primary efficacy assessment was the Physician's Lesion Assessment (PLA), a validated 4-ordinal scale. RESULTS The primary end point, the mean reduction in PLA grade from baseline to Day 106 was 1.7 for A-101 40%, 1.4 for A-101 32.5%, and 0.1 for vehicle (p < .001, both concentrations vs vehicle). Lesions for 68%, 62%, and 5% of subjects, respectively, were judged to be clear or near clear (p < .001, both concentrations vs vehicle). Local skin reactions were predominantly mild and transient. No subjects discontinued because of treatment-related adverse events. CONCLUSION A-101 solution demonstrated efficacy in treating SKs on the face. Greater magnitude of effect was seen with the 40% concentration than the 32.5% concentration. A-101 solution had a favorable safety and tolerability profile at both concentrations.


Mild hypothermia (32-34degC) treatment alleviates vital organ damage after cardiac arrest. A new cooling device, the Thermosuittrade operates by applying of a thin layer of water directly to the body surface. Hypothermic patients may experience sequential fibrillation. Therefore, we examined whether defibrillation could be administered safely and effectively in water. A 35 kg swine was anesthetized and placed inside the Thermosuittrade system. This consists of a water containing surround and pumping system. Conventional AED disposable defibrillation electrodes were applied to the animal's chest. Fibrillation was created by applying a 50-volt signal to a pacing wire introduced into the heart. Following a 30-second period of fibrillation, defibrillation was attempted using Medtronic AED 1000 defibrillator. Defibrillation voltage and current were measured. There were three test cases: dry in the system, wet in the functioning system, and damp. Cooling water in the system was contaminated with saline to simulate potential conditions in clinical application. In each fibrillation-defibrillation sequence, the heart was restarted successfully; this required less than 220 joules. Only a small difference was measured in the overall defibrillation voltage and current as applied to the electrodes for the different cases. Thus, underwater defibrillation is safe and can be performed effectively


method is not intrinsically more difficult than the arithmetic, and that it can be presented in a less abstract and consequently more easily intelligible way to the learner. If this is so, there are some strong reasons why the geometric method should be preferably adopted, one being that it can be learned at an earlier stage, and another that the two methods are independent, each serving to illustrate the other, and forming when combined a more complete and convincing whole than would result from the arithmetic method alone.


The factorial design technique is implemented to achieve greater accuracy in the determination of magnetic field distribution within a single cell of spin-exchange relaxation-free atomic magnetometer. Three-dimensional magnetic field distribution within a single vapor cell can be found by consecutively pumping, layer by layer, all the cell volumes perpendicular to the probe laser beam, detected by a photodiode array. Thus each element of the array collects information about the magnetic field in the small volume (voxel) which forms when the corresponding part of the probe beam and optically pumped layer cross. One of the most effective ways to enhance measurement accuracy is repeated pumping of the layers and averaging the measured results. However, the measurement time is multiplied several times due to the repeated scanning of the cell volume. The suggested technique enables increased measurement accuracy of each voxel while preserving the number of measurements. Magnetic field distribution is determined by the illumination of the cell layers one by one or simultaneously, according to a special algorithm, with subsequent multifactorial analysis of the obtained results.


Pigmentation of flowers in red is a very complex phenomenon. Various flower colors in many species have been shown to be due to genetic factors. Even if the necessary genes are present, however, synthesis of anthocyanin will not occur in a plant unless environmental conditions are favorable. Of environmental factors regulating anthocyanin formation, sunlight and temperature influence it directly in some plant tissues. To obtain flowers of good color under glasshouse conditions, temperature and light must be regulated by means of heating or cooling and supplementary lighting or shading, especially during the winter or summer season.The authors attempted in the study to obtain an information on the effects of temperature and sunlight on the coloration of rose flowers. The influence of temperature on the form of epidermal cells in the petal is also presented in this paper. As the materials, two varieties of garden roses were used. Using a variety of Hybrid Tea, Crimson Glory, the authors have followed the formation of red pigments quantitatively at various temperatures in the phytotron. After the differentiation of flower buds about 3 weeks after pruning, the potted plants were treated at various temperatures. At 20° and 10°C petals became dark red and showed a velvet-like appearance. According to anatomical observations, anthocyanin distributed only in the epidermis on the adaxial and abaxial surface of the petal. In the vertical section, the thickness of the upper epidermis of the petal treated at 20° and 10°C is much greater than that treated at 30°C. On the other hand, the upper epidermis showed a flat structure and red color did not appear at noon-and/or night-temperature of 30°C.In the experiment of the measurement of color, and the analysis of pigments in petals, the roses were treated at 13° and 23°C after the bud formation. At 23°C the petals have a purplish hue and become bluish purple red later. On the other hand, at 13°C they have a red hue and a lower luminosity, and become brown later. Paper chromatographic analysis showed that the anthocyanins in Crimson Glory variety are cyanin and chrysanthemin. Of these pigments, cyanin is the highest in content. The anthocyanin content of petals at 13°C is much higher than that treated at 23°C.Using a variety of Floribunda, Masquerade, an attempt was made in this paper to elucidate the effect of sunlight on the development of flower color. The flowers of the variety change their color ranging from yellow to red as the age of petals advances. Flower buds were covered with colored cellophane prior to their opening, which was removed after two weeks. Although the flowers bloomed, red color did not develop in their petals. Regardless of light quality, the anthocyanins were not formed at lower light intensity. It therefore appears that the flowers of Masquerade require high intensity of sunlight for development of their red color. There was a rise in anthocyanin content in the petals as the time advanced after flowering. In the petals of Masquerade, the anthocyanins are cyanin and chrysanthemin. Of the two anthocyanins, chrysanthemin has highly increased in content with advancing age of flowers.


Recent investigations have shown the metal-oxide-silicon field effect transistor (MOSFET) to be quite sensitive to radiation-induced surface effects.(1) The object of the present work was to obtain further experimental evidence toward identification of mechanisms responsible for device degradation. In particular, the time dependence of effects following both pulsed and steady-state irradiation was studied, since information is thereby provided on the type and concentration of radiation-dependent charge trapping states which affect device conductivity. Both intermediate and semipermanent conductivity changes following exposure to ionizing radiation were studied for three types of MOSFET's. These included n-channel enhancement, p-channel enhancement, and thin-film n-channel depletion units. Intermediate effects (referring to those whose time constants are typically 50 to 500 milliseconds following a radiation pulse of the order of 1 microsecond pulse width) were studied by means of observing drain current changes as a function of successive irradiations at various bias points. Both drain current changes and changes in transconductance were observed in the study of semi-permanent effects resulting from each irradiation.


The development of two sensory substitutions systems that provide cognitive feedback for FES (functional electrical stimulation) hand-grasp-restoration neuroprostheses is described. One system uses an array of five electrodes to provide machine status information and a spatially encoded representation of the command signal that a quadriplegic individual generates to achieve proportional grasp control. Only one electrode site is active at any given instant, and a second informational channel is superimposed on the spatial position channel by modulating the frequency of the stimulus pulses. The frequency-modulated feedback channel signals six levels of force developed at the finger tips during prehension activities. The second sensory system is an integral part of an implanted FES system and utilizes a single subdermally placed electrode to display machine status information and a five-level frequency code for feedback of the user-generated grasp control signal. The multielectrode feedback system was implemented for laboratory studies using surface-mounted electrodes, although its design will ultimately incorporate subdermal electrodes to provide a highly cosmetic and unencumbering system.<<ETX>>


In this study, leather was dyed using ultrasound and conventional methods to investigate the influence of ultrasound on leather dyeing. Ultrasound is more effective than mechanical agitation in enhancing leather dyeing. Effects of various process parameters, such as, dyeing temperature, dyeing time and doses of dye on dyeing of leather in presence of ultrasound were investigated. Dyed leathers were characterized with scanning electron microscopy (SEM), photomicrographic analysis, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), etc. It was observed that percentage exhaustion of dye, dye uptake, dye penetration and diffusion coefficient were increased significantly in presence of ultrasound compared to those of dyeing in absence of ultrasound. Moreover, physical properties of the dyed leathers were also investigated. Color rub fastness, perspiration, tensile strength, etc. of dyed leather in presence of ultrasound were higher than that of without ultrasound. SEM analyses of the surface and cross section of the dyed leather showed that fiber structure was not affected by ultrasound. Photomicrographic analysis of cross-section of the dyed leather also showed a deeper penetration of dye in presence of ultrasound. Consequently, dye content in the spent liquor was decreased resulting in a lower environmental pollution.


Knowledge-intensive NLP tasks can benefit from linking natural language text with facts from a Knowledge Graph (KG). Although facts themselves are language-agnostic, the fact labels (i.e., language-specific representation of the fact) in the KG are often present only in a few languages. This makes it challenging to link KG facts to sentences in languages other than the limited set of languages. To address this problem, we introduce the task of Multilingual Fact Linking (MFL) where the goal is to link fact expressed in a sentence to corresponding fact in the KG, even when the fact label in the KG is not available in the language of the sentence. To facilitate research in this area, we present a new evaluation dataset, IndicLink. This dataset contains 11,293 linked WikiData facts and 6,429 sentences spanning English and six Indian languages. We propose a Retrieval+Generation model, ReFCoG, that can scale to millions of KG facts by combining Dual Encoder based retrieval with a Seq2Seq based generation model which is constrained to output only valid KG facts. ReFCoG outperforms standard Retrieval+Re-ranking models by 10.7 pts in Precision@1. In spite of this gain, the model achieves an overall score of 52.1, showing ample scope for improvement in the task.ReFCoG code and IndicLink data are available at https://github.com/SaiKeshav/mfl


During human kidney development, cells of the proximal nephron gradually differentiate into podocytes and parietal epithelial cells (PECs). Podocytes are terminally differentiated cells that play a key role in both normal and pathological kidney function. Therefore, the potential of podocytes to regenerate or be replaced by other cell populations (PECs) is of great interest for the possible treatment of kidney diseases. In the present study, we analyzed the proliferation and differentiation capabilities of podocytes and PECs, changes in the expression pattern of nestin, and several early proteins including WNT4, Notch2, and Snail, as well as Ki-67, in tissues of developing, postnatal, and pathologically changed human kidneys by using immunohistochemistry and electron microscopy. Developing PECs showed a higher proliferation rate than podocytes, whereas nestin expression characterized only podocytes and pathologically changed kidneys. In the developing kidneys, WNT4 and Notch2 expression increased moderately in podocytes and strongly in PECs, whereas Snail increased only in PECs in the later fetal period. During human kidney development, WNT4, Notch2, and Snail are involved in early nephrogenesis control. In kidneys affected by congenital nephrotic syndrome of the Finnish type (CNF) and focal segmental glomerulosclerosis (FSGS), WNT4 decreased in both cell populations, whereas Notch2 decreased in FSGS. In contrast, Snail increased both in CNF and FSGS, whereas Notch2 increased only in CNF. Electron microscopy revealed cytoplasmic processes spanning the urinary space between the podocytes and PECs in developing and healthy postnatal kidneys, whereas the CNF and FSGS kidneys were characterized by numerous cellular bridges containing cells with strong expression of nestin and all analyzed proteins. Our results indicate that the mechanisms of gene control in nephrogenesis are reactivated under pathological conditions. These mechanisms could have a role in restoring glomerular integrity by potentially inducing the regeneration of podocytes from PECs.


Background: Primary cardiac lymphoma (PCL) is an extremely rare cardiac tumor and progresses rapidly, which often has short median survival time and poor prognosis unless diagnosed and treated in time.Case presentation: A 61-year-old man was admitted to hospital with repeated chest tightness and pain for 3 days and the right atrial mass by ultrasonography in the other hospital for 1 day. The echocardiography revealed an irregular hyperechoic mass in the right atrium with the size of the mass is about 5.3cm*4.3cm. Partial resection of right atrial tumor under general anesthesia and cardiopulmonary bypass was performed. After operation, enhanced chest computed tomography (CT) showed a mild enhancement mass in the right atrium. The histopathological examination revealed diffuse large B cell lymphoma. After careful examination, PCL was diagnosed and chemotherapy of low dose R-CHOP for 6 courses were used. After the last course, enhanced CT examination showed that the tumor almost disappeared and the patient's symptoms improved significantly.Conclusion: PCL is a extraordinarily rare disease with poor prognosis, and it is necessary to improve the awareness of this disease.Prompt diagnosis and timely chemotherapy in combination with surgery could lead to excellent clinical outcomes of the patient with PCL.


Anyone interested in the development of medical education in the United States under the influence of Thomas Jefferson and the origins of the School of Medicine at the University of Virginia, will be grateful to Dr. John Dorsey for his enthusiastic work in collecting and editing the Jefferson-Dunglison Correspondence. Dunglison, a young Englishman, was the first professor of medicine at the new university at Charlottesville. In the exchange of letters we see in intimate detail aspects of the twofold effect of Jefferson's influence on Dunglison and Dunglison's influence on Jefferson. Dunglison came as a very young man to head the school of medicine in Jefferson's "academical village." He came under the influence of the aging but alert Mr. Jefferson who was his patient during the last two years of his life, when he was treated for prostatic hypertrophy. We find the agreement under which Dunglison worked as a full-time clinical