bluuebunny/crossref_metadata_2025 huggingface dataset:
Proposal and Evaluation of Hybrid Encoding of CSP to SAT Integrating Order and Log Encodings
Authors: Soh Takehide , Banbara Mutsunori , Tamura Naoyuki
Published: March 2017

This paper proposes a new hybrid encoding of finite linear CSP to SAT which integrates order and log encodings. The former maintains bound consistency by unit propagation and works well for constraints consisting of small/middle sized arity and variable domains. The latter generates smaller CNF and works well for constraints consisting of larger sized arity and variable domains but its performance is not good in general because more inference steps are required to ripple carries. This paper describes the first attempt of hybridizing the order and log encodings without channeling constraints. Each variable is encoded by either the order encoding or the log encoding, and each constraint can contain both types of variables. Using the CSP solver competition benchmark consisting of 1458 instances, we made a comparison between the order, log and proposed hybrid encodings. As a result, the hybrid encoding solves the largest number of instances with the shortest CPU time. We also made a comparison with the four state-of-the-art CSP and SMT solvers Mistral, Opturion CPX, Yices, and z3. In this comparison, the hybrid encoding also shows the best performance. Furthermore, we found that the hybrid encoding is especially superior than other solvers for instances containing disjunctive constraints and global constraints — it indeed solves more instances than the virtual best solver consisting of those four state-of-the-art systems.
A Conventional Dialogue Model Based on Dialogue Patterns
Authors: Duplessis Guillaume Dubuisson , Pauchet Alexandre , Chaignaud Nathalie , Kotowicz Jean-Philippe
Published: March 2017

Our work aims at designing a dialogue manager dedicated to agents that interact with humans. In this article, we investigate how dialogue patterns at the dialogue act level extracted from Human-Human interactions can be fruitfully used by a software agent to interact with a human.We show how these patterns can be leveraged via a dialogue game structure in order to benefit to the dialogue management process of an agent. We describe how empirically specified dialogue games can be employed on both interpretative and generative levels of dialogue management. We present Dogma, an open-source module that can be used by an agent to manage its conventional communicative behaviour. We show that our library of dialogue games can be used into Dogma to generate fragments of dialogue that are strongly coherent from a human perspective.
Axial-Delayed Control of Nonlinear Resonance of Nanobeams with Graphene Sensor
Authors: Liu Canchang , Ding Qian , Gong Qingmei , Ma Chicheng , Yue Shuchang , Liu Lu
Published: March 2017

Nonlinear resonance response of an electrostatic-actuated nanobeam is controlled by using a delayed axial electrostatic force with near-half the natural frequency. A graphene sensor pasted on the surface of the nanobeam is used to extract the vibration voltage signal. An axial-delayed capacitive controller is designed to produce delayed axial force to control the nonlinear vibration of the nanobeam. The vibration voltage signal from the graphene sensor is input to the axial-delayed capacitive controller to attenuate the nonlinear vibration of the nanobeam. The dynamic response of the resonator is investigated by using the method of multiple scales directly. The sufficient conditions of guaranteeing the system stability and the saddle-node bifurcation are studied. The attenuation ratio is defined as the ratio of the peak amplitude of the nonlinear vibration system with control to that without control. A critical feedback gain is given, which can shift the frequency–amplitude curves from the nonlinear vibration to a linear vibration. An optimal method in which the attenuation ratio is taken as objective function and the aforementioned sufficient conditions as the constraint conditions is given to calculate the optimal feedback gains. Numerical simulations are conducted for uniform nanobeams.
Supporting Team Work in Game Design
Authors: Cappellini Giacomo , Maggiorini Dario , Ripamonti Laura Anna
Published: March 2017

Developing a video game is a costly activity, not only from an economic perspective, but also in terms of the time devoted to researching innovative solutions and managing interfaces between the creative and technical team members. In this article, we explore the possibility to use an approach rooted into AI techniques (namely Behaviour Trees) to help establish a lingua franca between these two different functions, in order to optimize both the development time and the quality of the final product. In particular, we have developed BETTER, a middleware which can be easily embedded into any game engine, and tested it during the design and development of Crazy-Hill, a commercial video game for iOS-based mobile devices.
Oscillatory synchrony between head direction cells recorded bilaterally in the anterodorsal thalamic nuclei
Authors: Butler William N. , Taube Jeffrey S.
Published: March 2017

The head direction (HD) circuit is a complex interconnected network of brain regions ranging from the brain stem to the cortex. Recent work found that HD cells corecorded ipsilaterally in the anterodorsal nucleus (ADN) of the thalamus displayed coordinated firing patterns. A high-frequency oscillation pattern (130–160 Hz) was visible in the cross-correlograms of these HD cell pairs. Spectral analysis further found that the power of this oscillation was greatest at 0 ms and decreased at greater lags, and demonstrated that there was greater synchrony between HD cells with similar preferred firing directions. Here, we demonstrate that the same high-frequency synchrony exists in HD cell pairs recorded contralaterally from one another in the bilateral ADN. When we examined the cross-correlograms of HD cells that were corecorded bilaterally, we observed the same high-frequency (~150- to 200-Hz) oscillatory relationship. The strength of this synchrony was similar to the synchrony seen in ipsilateral HD cell pairs, and the degree of synchrony in each cross-correlogram was dependent on the difference in tuning between the two cells. Additionally, the frequency rate of this oscillation appeared to be independent of the firing rates of the two cross-correlated cells. Taken together, these results imply that the left and right thalamic HD network are functionally related despite an absence of direct anatomical projections. However, anatomical tracing has found that each of the lateral mammillary nuclei (LMN) project bilaterally to both of the ADN, suggesting the LMN may be responsible for the functional connectivity observed between the two ADN.

NEW & NOTEWORTHY This study used bilateral recording electrodes to examine whether head direction cells recorded simultaneously in both the left and right thalamus show coordinated firing. Cross-correlations of the cells’ spike trains revealed a high-frequency oscillatory pattern similar to that seen in cross-correlations between pairs of ipsilateral head direction cells, demonstrating that the bilateral thalamic head direction signals may be part of a single unified network.
Sustainable Management of Calcareous Saline-Sodic Soil in Arid Environments: The Leaching Process in the Jordan Valley
Authors: Batarseh Mufeed
Published: March 2017

A leaching experiment of calcareous saline-sodic soil was conducted in Jordan Valley and aimed to reduce the soil salinity ≤ 4.0 dS m−1. The quantification of salt removal from the effective root zone was done using three treatment scenarios. Treatment A contained soil amended with gypsum leaching with fresh water (EC = 1.1 dS m−1). Treatments B and C contained nonamended soil, but B was leached with fresh water only while treatment C’s soil was washed with saline agricultural drainage water (EC = 8 dS m−1) at the start of the experiment and continued with fresh water to reach the desired soil salinity. All treatments were able to reduce the soil salinity to the desired level at the end of the experiment; however, there were clear differences in the salt removal efficiencies among the treatments which were attributed to the presence of direct source of calcium ion. The soil amended with gypsum caused a substantial decline in soil salinity and drainage water’s electrical conductivity and drained the water twice as fast as the nonamended soil. It was found that utilizing agricultural drainage water and gypsum as a soil amendment for calcareous saline-sodic soil reclamation can beneficially contribute to sustainable agricultural management in the Jordan Valley.
Surface Area of Patellar Facets: Inferential Statistics in the Iraqi Population
Authors: Al-Imam Ahmed , Al-Zamili Zaid , Omar Rawan
Published: March 2017

Background. The patella is the largest sesamoid bone in the body; its three-dimensional complexity necessitates biomechanical perfection. Numerous pathologies occur at the patellofemoral unit which may end in degenerative changes. This study aims to test the presence of statistical correlation between the surface areas of patellar facets and other patellar morphometric parameters. Materials and Methods. Forty dry human patellae were studied. The morphometry of each patella was measured using a digital Vernier Caliper, electronic balance, and image analyses software known as ImageJ. The patellar facetal surface area was correlated with patellar weight, height, width, and thickness. Results. Inferential statistics proved the existence of linear correlation of total facetal surface area and patellar weight, height, width, and thickness. The correlation was strongest for surface area versus patellar weight. The lateral facetal area was found persistently larger than the medial facetal area, the p value was found to be <0.001 (one-tailed t-test) for right patellae, and another significant p value of < 0.001 (one-tailed t-test) was found for left patellae. Conclusion. These data are vital for the restoration of the normal biomechanics of the patellofemoral unit; these are to be consulted during knee surgeries and implant designs and can be of an indispensable anthropometric, interethnic, and biometric value.
Predictors of Time-to-Contraceptive Use from Resumption of Sexual Intercourse after Birth among Women in Uganda
Authors: Wamala Robert , Kabagenyi Allen , Kasasa Simon
Published: March 2017

Globally, there is extant literature on patterns and dynamics of postpartum contraceptive use with hardly any evidence examining time-to-contraceptive use from resumption of sexual intercourse after birth among women in Uganda. Methods. The analysis was based on data from 2011 Uganda Demographic and Health Survey on a sample of 2983 married women with a birth in the past three years preceding the survey and had resumed sexual intercourse. A time-to-contraceptive use was adopted in the analysis using life tables based on the Kaplan-Meier estimates, while the Log-Rank Chi-square tests assessed the variables to be included in regression analysis. Cox-Proportional Hazard regression was run to identify the predictors of time-to-contraceptive use among postpartum women in Uganda. Sampling weights were applied in the analysis to ensure representativeness. Results. The median time-to-contraceptive use was 19 months (range 0–24). Time to adoption of modern contraceptive use was significantly longer among women with no formal education, residing in northern region, who (HR=0.56, CI: 0.40–0.78) had delivered at home/traditional birth attendant (HR=0.75, CI: 0.60–0.93), had 1–3 antenatal care visits (HR=0.83, CI: 0.70–0.98), and were in poorest wealth quintile. Conclusions. Measures for enhancing modern contraceptive use during and after the postpartum period should focus on (i) addressing hindrances in accessing family planning, particularly among poor and noneducated women; (ii) integration of family planning service delivery into routine ANC through counseling; and (iii) promoting deliveries in health facilities.
Consensus Control for a Multiagent System with Time Delays
Authors: Cao Yiran , Oguchi Toshiki , Verhoeckx Paul , Nijmeijer Henk
Published: March 2017

In this paper, we consider the consensus control problem for a multiagent system (MAS) consisting of integrator dynamics with input and output time delays. First, we investigate a consensus condition for the MAS with a linear controller and without any delay compensation. We then propose a consensus controller with a state predictor to compensate the effect of time delay. The consensus condition for this controller is derived and investigated. Finally, we present an example of solving the consensus control problem for two‐wheel mobile robots with feedback loops that pass through a computer network with time delays. To demonstrate the validity of the predictor‐based controller, we conduct experiments with two‐wheel mobile robots and present the results.
Construction of Expression Shuttle Vectors for the HaloarchaeonNatrinemasp. J7 Based on Its Chromosomal Origins of Replication
Authors: Wang Yuchen , Chen Beibei , Sima Linshan , Cao Mengzhuo , Chen Xiangdong
Published: March 2017

HaloarchaeonNatrinemasp. J7, the first reported archaeon harboring both plasmid and chromosome-based temperate viruses, is a useful model for investigating archaeal virus-host and virus-virus interactions. However, the lack of genetic tools has limited such studies. On the basis of the automatically replicating sequences of the J7 chromosome and thepyrFmarker, we constructed seven vectors, six of which were confirmed to possess replication ability in apyrF-deletion derivative of J7 (J7-F). Among these vectors, pFJ1, pFJ4, and pFJ6 could be transformed into the host strain with relatively high efficiency (approximately 103colony-forming units/μg DNA) and were present at about one copy per chromosome. These three vectors could be stably maintained in J7-F without selection and were used for heterologous protein expression. Only pFJ6 was found to be present in the transformed cells in an exclusively episomal, nonintegrated state (one copy per chromosome). In contrast, some pFJ1 and pFJ4 DNA was probably integrated into the J7-F chromosome. In addition, pFJ6 was found to be compatible with pYCJ in J7 cells, suggesting that these two vectors could be used for further studies of virus-virus and virus-host interactions.
Metabolomic Signature of Coronary Artery Disease in Type 2 Diabetes Mellitus
Authors: Stratmann Bernd , Richter Katrin , Wang Ruichao , Yu Zhonghao , Xu Tao , Prehn Cornelia , Adamski Jerzy , Illig Thomas , Tschoepe Diethelm , Wang-Sattler Rui
Published: March 2017

Coronary artery disease (CAD) is a common complication of type 2 diabetes mellitus (T2D). This case-control study was done to identify metabolites with different concentrations between T2D patients with and without CAD and to characterise implicated metabolic mechanisms relating to CAD. Fasting serum samples of 57 T2D subjects, 26 with (cases) and 31 without CAD (controls), were targeted for metabolite profiling of 163 metabolites. To assess the association between metabolite levels and CAD, partial least squares (PLS) analysis and multivariate logistic regression analysis with adjustment for CAD risk factors and medications were performed. We observed a separation of cases and controls with two classes of metabolites being significantly associated with CAD, including phosphatidylcholines, and serine. Four metabolites being independent from the common CAD risk factors displaying best separation between cases and controls were further selected. Addition of the metabolite concentrations to risk factor analysis raised the area under the receiver-operating-characteristic curve from 0.72 to 0.88 (p=0.020), providing improved sensitivity and specificity for CAD classification. Serum phospholipid and serine levels independently discriminate T2D patients with and without CAD. Oxidative stress and reduced antioxidative capacity lead to lower metabolite concentrations probably due to changes in membrane composition and accelerated phospholipid degradation.
Abstract A07: Detection of structural variants and recurrent breakpoint genes in colorectal adenoma-to-carcinoma progression
Authors: Broek Evert van den , Dijkstra Maurits J.J. , Voorham Quirinus J.M. , Carvalho Beatriz , Wiel Mark A. van de , Abeln Sanne , Meijer Gerrit A. , Fijneman Remond J.A.
Published: March 2017

Background and Aim: The transition of pre-malignant colorectal adenomas (CRAs) into malignant colorectal carcinomas (CRCs) is accompanied by accumulation of somatic genetic alterations. The contribution of small nucleotide variants (SNVs, such as gene point mutations) and numerical DNA copy number aberrations (CNAs, such as gains and losses of large chromosomal segments) in tumor genomes has been studied extensively. In contrast, studies that systematically detect recurrent structural variants (SVs, such as chromosomal breaks) across large series of clinically well-defined samples are scarce. We recently developed “GeneBreak”, a computational method to identify genes that are recurrently affected by the genomic location of CNA-associated chromosomal breaks, and demonstrated high prevalence and clinical relevance of recurrent breakpoint genes in advanced CRCs (PLoS One 2015;10(9):e0138141). Using a similar approach, the present study aimed to determine what recurrent breakpoint genes contribute to colorectal adenoma-to-carcinoma progression.

Methods: Differences in somatic CNA-associated gene breakpoint frequencies in 466 CRC and 118 CRA samples were examined using high-resolution array-comparative genomic hybridization (aCGH) profiles. Pearson's Chi-square statistic was applied to determine differences in gene breakpoint frequencies between CRC and CRA samples.

Results: In total 21 recurrent breakpoint genes were more frequently affected in CRCs compared to CRAs (p<0.05). MACROD2 was affected by chromosomal breakpoints in 40% of CRCs while not being affected in CRAs. The frequencies of SVs in the other 20 recurrent breakpoint genes ranged from 5% to 29% in CRCs, and from 0% to 2% in CRAs.

Conclusion: We identified 21 recurrent breakpoint genes that are frequently affected by SVs in CRCs but not in CRAs. Additional studies are needed to further elaborate the biological and clinical role of these 21 candidate driver genes for colorectal tumor progression.

Citation Format: Evert van den Broek, Maurits J.J. Dijkstra, Quirinus J.M. Voorham, Beatriz Carvalho, Mark A. van de Wiel, Sanne Abeln, Gerrit A. Meijer, Remond J.A. Fijneman. Detection of structural variants and recurrent breakpoint genes in colorectal adenoma-to-carcinoma progression. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr A07.
Abstract A08: Extensive subclonal mutations in human colorectal cancers detected by Duplex Sequencing
Authors: Fox Edward John Paul , Schmitt Michael W. , Reid-Bayliss Kate S. , Beckman Robert A. , Loeb Lawrence A.
Published: March 2017

The accumulation of somatic mutations is a defining hallmark of cancer. The genomes of solid tumors contain thousands of mutations that are present in most or all of the malignant cells in that tumor. In addition to these clonal mutations, subclonal mutations, those occurring only in a fraction of malignant cells, likely contribute to the phenotypic and morphologic heterogeneity of cancer cells within a tumor. The extent of subclonal mutations in cancer, however, has been difficult to quantify, as the high error rate of next-generation sequencing precludes reliable detection of mutations present in fewer than 5% of cells. Here, we apply the highly accurate Duplex Sequencing methodology to quantify the extent of subclonal mutations in colorectal cancer (CRC) and paired normal mucosa. By sequencing known CRC driver and non-driver genes, we find that colorectal cancers without known DNA repair deficits harbor an extensive complement of subclonal mutations, in addition to the large number of clonal mutations previously identified. We show that normal colonic mucosa also accumulates substantial numbers of subclonal mutations in an age-dependent manner. The frequency of tumor-associated subclonal mutations, however, does not correlate with age, and has a spectrum distinct from that seen in normal tissue, indicating different mechanisms of mutation accumulation are operative in normal and tumor tissue. The frequency of tumor cells harboring unique subclonal mutations is so high that it is likely that every possible neutral somatic point mutation is present by the time a tumor is clinically detectable. We propose that these subclonal mutations likely accumulate in a series of punctuated bursts, making it highly likely that resistant subclones will emerge during chemotherapy.

Citation Format: Edward John Paul Fox, Michael W. Schmitt, Kate S. Reid-Bayliss, Robert A. Beckman, Lawrence A. Loeb. Extensive subclonal mutations in human colorectal cancers detected by Duplex Sequencing. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr A08.
Abstract A19: Silencing LEF1 decreases the resistance of colorectal cancer cell lines to 5-FU as common chemotherapeutic drug
Authors: Teimoori-Toolabi Ladan , Fakhr Elham , Zare Fatemeh
Published: March 2017

Wnt signaling pathway is assumed to be the most important pathway activated in colorectal cancer. As this pathway in addition to Notch and hedgehog signaling pathway is responsible for the maintenance of stem cells in the population of cancerous cells, it could be predicted that by silencing this pathway the resistance of cancerous cells to chemotherapeutic drugs would be decreased. In this regard we tried to silence LEF1 as an important component of this pathway in two colorectal cancer cell lines and see the response of transfected cells to 5-flurouracil.

Oligonucleotide for silencing LEF1 was constructed and inserted into pSilencer Neo2.1 (Invitrogen). Thereafter these constructed were stably transfected to HCT116 and SW480 as colorectal cancer cell lines after treating the transfected cells with G418 for 21 days. Response of these cells to 5-flurouracil as a common chemotherapeutic drug was studied by MTT proliferation assay. The expression of LEF1 in transfected and non-transfected cells was also studied by Quantitative PCR. Cell cycle analysis was done by staining the cells with PI and analyzing them by flowcytometry instrument.

While the expression of LEF1 in SW480 transfected with pSilencer-antiLEF1 reduced to 0.004 in comparison to non-transfected cells in HCT116 cells transfected with pSilencer-anti LEF1 this value was 0.000002 in comparison to non-transfected cells.

Whereas the LC50 of 5-Flurouracil on non-transfected HCT116 and SW480 for 5-FU were 0.55 ng/µl and 1.45 ng/µl respectively. These values in transfected cells reduced to 0.18 and 0.1 ng/µl respectively. The percentages of proliferating cells (G2+S) stably transfected cells reduced to 30% and 32% in comparison to 39% and 45% in SW480 and HCT116 cell lines respectively.

These findings showed that silencing LEF1 as a main component of wnt signaling pathway sensitizes HCT116 and SW480 cells to 5-flurouracil. The difference between sensitizing strength may be due to mutations in other components of wnt signaling pathway or mutations in other genes like p53 and k-ras which is dissimilar between HCT116 and SW480 cells. This modality can be considered as sensitizing agents adjuvant to other chemotherapeutic drugs like 5-FU.

Note: This abstract was not presented at the conference.

Citation Format: Ladan Teimoori-Toolabi, Elham Fakhr, Fatemeh Zare. Silencing LEF1 decreases the resistance of colorectal cancer cell lines to 5-FU as common chemotherapeutic drug. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr A19.
Abstract B06: Cathepsin B expression in colorectal cancer in Middle East population: Potential value as a tumor biomarker for late stages
Authors: Abdulla Maha
Published: March 2017

Objective: To investigate Cathepsin B (CTSB) expression in colorectal cancer (CRC) tissues and serum, the association of CTSB expression with tumor stages and metastasis and targeting CTSB by nanoparticles for potential CRC therapeutics.

Methods: CTSB expression was determined in 100 pairs of CRC tumor and adjacent normal tissue using quantitative PCR for mRNA levels. Serum CTSB levels were evaluated in 95 patients and 20 healthy control using enzyme-linked immunosorbant assay (ELISA) technique. Detection of Cathepsin B protein expression in tissues was done using immunohistochemistry and western blotting. Cathepsin B protein expression was inhibited using cobalt oxide nanoparticles in human colorectal cancer cells.

Results: Greater than 90% of tumors had detectable CTSB protein expression with significant increase staining in tumors compared with matched normal colon (p=0.006). The relative levels of CTSB mRNA in tumor samples and adjacent normal colorectal tissue were 0.04 ± 0.06 and 0.01 ± 0.02 respectively. The mRNA expression in early stage CRC compared to late stage CRC was 0.05 ± 0.04 and 0.02 ± 0.01, respectively. Increased mRNA expression was seen in the advanced stages with lymph node metastases compared to control P=0.002. CTSB was significantly higher in sera of patients with lymph node metastasis compared to early and late stage primary tumors. A subset of 40 paired tissue extracts were analyzed by western blotting. This also revealed consistent increase of CTSB protein level in tumor tissue. Treatment of human CRC cell HT-29 with increasing concentrations of cobalt oxide nanoparticles resulted in significant decrease of CTSB expression.

Conclusion: These findings thus indicate that CTSB may be an important prognostic biomarker for early stage CRC and lymph node metastasis in Middle East populations. Monitoring serum CTSB in CRC patient may predict and diagnose lymph node metastasis. Furthermore CTSB may represent a potential target for nanoparticle-based drugs in the treatment of colorectal cancer.

Citation Format: Maha Abdulla. Cathepsin B expression in colorectal cancer in Middle East population: Potential value as a tumor biomarker for late stages. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B06.
Abstract B08: Potential biomarkers for colorectal cancer diagnosis and prognosis
Authors: Mansour Hicham , Bouarourou Noureddine , Roperch Jean Pierre , Habib Fouazi , Said Mourad
Published: March 2017

Colorectal cancer (CRC) is one of the most common cancers worldwide. It harbors several genetic and epigenetic alterations, which makes finding suitable biomarkers a challenge. CRC Cell lines are invaluable biomedical research tools for drug screening and biomarker discovery. Two emblematic cell lines for CRC were extensively used, HT29 and HCT116. We performed the whole transcriptome sequencing of these two cell lines and two normal epithelial cell lines, CR1780 and CRL18, derived from the colon as control. A methylation quantification of downregulated genes enables to screen potential biomarkers, which could be used as potential biomarkers for CRC diagnosis and prognosis.

Method: Total RNA was extracted from HT29, HCT116, CR1780 and CRL18 using RNeasy Mini Kit (Qiagen). mRNA libraries were generated using TruSeq Stranded mRNA Library Prep Kit (Illumina), and high-throughput sequencing were performed using Illumina systems (Hiseq and Miseq). All reads were filtered for high-quality reads (≥Q30, adapters trimming and broken pair-reads removing). Reads alignment and genes profiling analysis were done with CLCbio software. Selected genes downregulated with p-value <0.001 in cancer cell lines versus normal cell lines, were evaluated for methylation in DNA extracted from tumors and autologous normal tissues from CRC patients.

Results: The transcriptome analysis reveals 741 different splice variants are downregulated in both cancer cell lines HT29 and HCT116, when compared to the two normal cell lines, CR1780 and CRL18 (p-value <0.001). 10 relevant downregulated genes were selected, ACTG2, THY1, IGFBP3, WNT2, RAB32, SPARC, COL1A, MMP2, IGFBP3 and VIM. Interestingly, all the splice variants (10) of Vim, 7 of ATG2, 4 of THY1 and 2 of IGFBP3 were dramatically downregulated. Methylation quantification demonstrates the hypermethylation of all these 10 downregulated genes, in the tumors compared to matched normal tissues.

Conclusion. At the level of mRNA expression and methylation, this study enables to screen potential biomarkers for CRC diagnosis and prognosis.

Citation Format: Hicham Mansour, Noureddine Bouarourou, Jean Pierre Roperch, Fouazi Habib, Mourad Said. Potential biomarkers for colorectal cancer diagnosis and prognosis. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B08.
Abstract B15: Anti-metastatic activity of RGD-specific cadherin-17-targeting monoclonal antibodies in colorectal cancer
Authors: Bartolomé Rubén , Torres Sofia , Escudero-Paniagua Beatriz , Aizpurua Carmen , Calviño Eva , Imbaud Juan I. , Casal Ignacio
Published: March 2017

Most colorectal cancer deaths occur as a consequence of late diagnosis and the appearance of metastasis. We demonstrated that a RGD motif present in liver-intestine cadherin, also known as cadherin 17 (CDH17), plays a critical role in the liver metastasis of colorectal cancer by interacting with α2β1 integrin. CDH17 is able to induce a conformational change in β1 integrin to promote a high affinity conformation. This change is dependent of the RGD motif present in domain 6 of CDH17. The same activation was observed after cell exposition to 9 amino acid peptides containing the RGD motif and the flanking sequences from CDH17. Commercial antibodies anti-CDH17 did not cause any effect on β1 integrin activation. Here, we have used peptides containing the RGD motif and their flanking sequences in CDH17 to retrieve four highly selective monoclonal antibodies with anti-metastatic activity. Only CDH17 RGD-specific monoclonal antibodies inhibited β1 integrin activation in colorectal cancer cells. This inhibition provoked a significant reduction in cell adhesion and proliferation of metastatic cells. In addition, the treatment with these four anti-cadherin RGD antibodies impaired the activation of FAK, JNK and ERK kinases, which are critical for cell adhesion and proliferation. Moreover, RGD-specific monoclonal antibodies were able to cause a significant increase in mouse survival after intra-splenic injection together with highly metastatic cells, as determined by Kaplan-Meier survival analysis and log-rank curves. However, this effect on survival was different for each monoclonal antibody, suggesting a relevant impact of the RGD binding orientation in antibody recognition. As a conclusion, we propose that blocking the interaction between RGD cadherins and α2β1 integrin with highly selective monoclonal antibodies constitutes a promising therapy against colon cancer progression and liver metastasis.

Citation Format: Rubén Bartolomé, Sofia Torres, Beatriz Escudero-Paniagua, Carmen Aizpurua, Eva Calviño, Juan I. Imbaud, Ignacio Casal. Anti-metastatic activity of RGD-specific cadherin-17-targeting monoclonal antibodies in colorectal cancer. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B15.
Abstract B16: Activation of NRF2 and adaptive resistance to chemotherapy
Authors: Clinton Sarah A. , Barbour Karen W. , Berger Franklin G.
Published: March 2017

Nuclear factor-erythroid-2-related factor 2 (NRF2), a member of the cap ‘n’ collar family of bZIP transcription factors, confers protection against oxidative and electrophilic stress. NRF2 is of great interest in cancer research, due to its role in response to chemotherapy, including the class of drugs targeting thymidylate synthase (TYMS). It has long been known that inhibition of TYMS leads to depletion of thymidine levels and the onset of programmed cell death, deriving from the enzyme's function as the sole de novo source of thymidine for DNA replication and repair. Exposing cells to TYMS inhibitors such as fluoropyrimidine antimetabolites (5-fluorouracil, or FUra; 5'-fluoro-2'-deoxyuridine, or FdUrd), as well as anti-folate analogs (raltitrexed, or RTX), induce intracellular concentrations of reactive oxygen species, which are a primary cause of drug-mediated toxicity. This prompted our focus on assessing the impact of NRF2 on cellular response to TYMS inhibitors. Using human colon tumor-derived cell line HCT116, we have shown by gene expression profiling that drug exposure induces expression of a number of genes that are modulated by NRF2. Quantitative PCR assays of several colon tumor cell lines verified that FUra, FdUrd, and RTX induce transcription of several genes known to be NRF2-targets, including AKR1B10, ALDH3A1, HSPB8, HMOX1, and SERPINE1, among others. Such induction mirrors that in response to the known NRF2 activator tert-butylhydroquinone (tBHQ). NRF2 protein concentration and nuclear localization are increased by FdUrd treatment, though not to the same extent as with tBHQ. Reporter gene constructs were used to show that both FdUrd and tBHQ induce transcription mediated by the NRF2-binding antioxidant response element (ARE). Furthermore, chromatin-immunoprecipitation experiments revealed that TYMS inhibitors promote occupancy of the ARE regions of several genes by NRF2; again, tBHQ had a much greater effect. Further analysis showed an association between gene induction by TYMS inhibitors and patterns of histone acetylation within the NRF2-binding ARE regions. Finally, we observed that increases in the apoptotic index following exposure to TYMS inhibitors were greater in cells in which the transcription factor was subjected to siRNA-mediated “knockdown” or CRISPR/Cas9-mediated “knockout”, indicating that reduced NRF2 expression sensitizes cells to TYMS inhibitors. Overall, we conclude that TYMS inhibitors activate NRF2 and its downstream target genes, thereby constraining drug response. Reducing such activation of NRF2 or its consequences may be an effective strategy to sensitizing tumor cells to chemotherapy.

Citation Format: Sarah A. Clinton, Karen W. Barbour, Franklin G. Berger. Activation of NRF2 and adaptive resistance to chemotherapy. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B16.
Abstract B21: PDE10A overexpression in colon cancer cells and tumors relative to normal colonocytes and colon mucosa
Authors: Lindsey Ashley S. , Lee Kevin , Andrews Joel , Chang Wen-Chi L. , Ramirez-Alcantara Veronica , Tan Marcus , Grizzle William , Clapper Margie L. , Piazza Gary
Published: March 2017

Phosphodiesterase 10A (PDE10A) is a cGMP and cAMP degrading PDE isozyme expressed in areas of the brain controlling motor function and cognition. PDE10A has been strongly linked to diseases such as schizophrenia and Huntington's disease, for which PDE10A inhibitors are currently in clinical trials and appear to be well tolerated. Although, PDE10A has limited expression and no known function in peripheral tissues, high levels were measured in colon tumor cells in vitro and in vivo compared with cells derived from normal colon and colonic mucosa (Li et al., Oncogene 2015). PDE10A inhibition by small molecules or genetic silencing attenuated colon tumor cell growth by a mechanism involving cGMP/PKG activation, the suppression of oncogenic β-catenin, and a decrease in TCF transcriptional activity (Li et al., Oncogene 2015). These observations suggest that PDE10A may play an unrecognized role in tumorigenesis and provide a novel therapeutic target for colorectal cancer chemoprevention or therapy. The human colon tumor cell lines, HCT116, HT29, Caco2, and SW480, show elevated expression of PDE10A as compared to the normal colon mucosal epithelial cell line, NCM460, and are more sensitive to PDE10 inhibitors relative to NCM460 cells. Subcutaneous tumors established from HT29 colon tumor cells in athymic mice expressed elevated levels of PDE10A as compared to normal mouse colon tissue. Colon tumors collected from heterozygous APCmin/+FCCC mice displayed an elevation in PDE10A levels as compared to uninvolved mucosa from the APCmin/+FCCC mice and wild type colon mucosa. Overexpression of PDE10A mRNA and protein levels was also observed in colon adenocarcinomas relative to uninvolved colon mucosa in specimens obtained from colorectal cancer patients. These observations, along with recent findings that a novel sulindac derivative (ADT-061) with PDE10A inhibitory activity suppresses tumor formation in the APCmin/+FCCC mouse model of colon cancer without apparent toxicity, suggests that PDE10A provides a novel therapeutic target for cancer cell specific inhibition of tumor growth.

Citation Format: Ashley S. Lindsey, Kevin Lee, Joel Andrews, Wen-Chi L. Chang, Veronica Ramirez-Alcantara, Marcus Tan, William Grizzle, Margie L. Clapper, Gary Piazza. PDE10A overexpression in colon cancer cells and tumors relative to normal colonocytes and colon mucosa. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B21.
Abstract B25: Black-white differences in colorectal cancer screening and incidence over time by age and sex
Authors: Fedewa Stacey A. , Corley Douglas , Jemal Ahmedin , Siegel Rebecca , Goodman Michael , Doubeni Chyke
Published: March 2017

Introduction: Blacks have the highest colorectal cancer (CRC) burden of any racial/ethnic group and the underlying reason for this disparity has not been fully elucidated. Continued examination of incidence in relation to screening, which is recommended for men and women beginning at age 50 years, may provide valuable insights into these disparities. The present study examined black-white differences in CRC incidence and screening patterns by age and sex over time.

Methods: National Health Interview Surveys between 2000-2015 were used to estimate screening prevalence and prevalence ratios (PR) among adults 50 years and older by non-Hispanic white/black race and sex. Data from the SEER were used to estimate age-sex-specific incidence rates from 1992-2013.

Results: From 2000 to 2015, CRC screening prevalence in age 50 years and older increased by 69% in whites (from 39.4% to 66.5%) and by 98% in blacks (from 31.1% to 61.4%) on a relative scale. Increases in CRC screening were evident in both men and women. During this time period, black-white differences also narrowed, such that CRC screening in blacks was 19% lower than in whites in 2000 (PR=0.81, 95%CI 0.71,0.92) but only 6% lower in 2015 (PR=0.94, 95%CI 0.88, 1.00). Absolute black-white differences in CRC incidence rates were slightly larger for men than for women (men: 3.0-6.0 versus women: 2.8-5.4 per 100,000) in people 35-49 years old, but decreased overtime in both groups. In 50-79-year-olds, absolute black-white incidence differences were larger for men prior to 2003 (men: 19.8-28.9 versus women: 28.3-33.1 per 100,000) and during 2004-2013 (men: 27.7-53.3 versus women: 20.6-38.7 per 100,000). In 35-49-year-olds, black-white incidence rate ratios (IRR) decreased overtime from 1992-2000 to 2009-2013 in both men (1.47 to 1.19) and women (1.49 to 1.17), but increased in both men (1.06 to 1.38) and women (1.15 to 1.49) for those 50 years and older.

Conclusions: Black-white differences in CRC incidence in both absolute and relative terms are greatest in screening-eligible adults and have persisted in recent years whereas absolute differences in incidence in those younger than 50 are relatively small. These patterns may reflect racial gaps in screening uptake. However, disparities in CRC screening prevalence have narrowed in recent years and may portend convergence in CRC incidence rates.

Note: This abstract was not presented at the conference.

Citation Format: Stacey A. Fedewa, Douglas Corley, Ahmedin Jemal, Rebecca Siegel, Michael Goodman, Chyke Doubeni. Black-white differences in colorectal cancer screening and incidence over time by age and sex. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B25.
Abstract B26: Baseline serum albumin as a prognostic actor in patients with stage I and II colon adenocarcinoma
Authors: Gonzalez-Trejo Sagrario , Carrillo Jose F. , Carmona-Herrera Doris , Herrera-Goepfert Roberto , Ochoa-Carrillo Francisco J. , Aiello-Crocifoglio Vincenzo , Gallardo-Rincon Dolores , Onate-Ocana Luis F.
Published: March 2017

Background: Patients with stage I or II Colon carcinoma (CC) have a significant risk of recurrence after adequately performed curative resection. Adjuvant chemotherapy has not improved recurrence or survival in such patients. In this study, a prognostic model in patients with stage I or II CC, based on Baseline serum albumin (BSA) and other common clinical markers is presented.

Methods: Consecutive cases with CC treated at a single cancer center in Mexico City from January 1998 to December 2014, with diagnosis of adenocarcinoma by colonoscopy and biopsy were included in this cohort. Clinical history and chemistry data were registered, and patients were treated according to standard guidelines. Follow-up continued until June 2016; the Kaplan-Meier method and the Cox model were used to analyze the association of prognostic factors and overall survival (OS), and Hazard ratios (HR) were calculated.

Results: 1,259 cases of CC were treated, but only 496 patients have stage I and II CC and were included in the database: 234 women (47.2%) and 262 males (52.8%) and their mean age was 59.9 years (SD 14.9); 96, 339, 31 and 30 cases were pTNM stages I, IIa, IIb and IIc, respectively. BSA (HR 2.185), male gender (HR 1.43), baseline hemoglobin (HR 0.916), baseline platelet count (HR 0.998), baseline neutrophil count (HR 1.085), albumin/globulin ratio (HR 0.197), baseline platelet/lymphocyte ratio (HR 1.001), body mass index (HR 0.958), TNM stages (IIa HR 1.74, IIb HR 2.08, IIc HR 2.59; Stage I is the reference category), use of adjuvant chemotherapy (HR 0.465) and R classification (R1 HR 1.306, R2 HR 2.55, no resection HR 6.93; R0 is the reference category). Predicted survival functions using this model, defined 4 risk groups that showed better prognostic value than simple TNM stages I-IIc.

Conclusion: BSA is an independent, significant, simple, cheap and widely available prognostic factor in patients with CC. BSA and other clinical factors add significant prognostic information to TNM classification. Feasibly, it can be used to develop multivariate prognostic models with clinical impact defining the use of adjuvant chemotherapy. The use of histopathological and immunohistochemical markers could improve the prognostic information of this model.

Citation Format: Sagrario Gonzalez-Trejo, Jose F. Carrillo, Doris Carmona-Herrera, Roberto Herrera-Goepfert, Francisco J. Ochoa-Carrillo, Vincenzo Aiello-Crocifoglio, Dolores Gallardo-Rincon, Luis F. Onate-Ocana. Baseline serum albumin as a prognostic actor in patients with stage I and II colon adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B26.
Abstract IA04: The carcinogenic potential of bacterial biofilms
Authors: Sears Cynthia L.
Published: March 2017

The colonic microbiome is hypothesized to contribute to CRC pathogenesis and to potentially act as an initiator of colon oncogenesis, in part via induction of specific mucosal pro-carcinogenic immune responses. Both we and others have presented data from experimental models implicating specific bacteria in colon carcinogenesis. Enterotoxigenic Bacteriodes fragilis (ETBF), Escherichia coli containing the pks island [E. coli (pks)] and Fusobacterium nucleatum represent colon carcinogenic bacteria strongly implicated to date in both experimental models and human disease. To further address the links between the microbiota and human colon cancer, we are prospectively studying the microbial associations of human CRC together with parameters of mucosal immunity. Paired surgical CRC samples and normal colon mucosa are studied along with colon biopsies (right and left) of healthy controls undergoing screening colonoscopy. We have presented data demonstrating that sporadic colon tumors located proximal to the hepatic flexure are characterized by invasive polymicrobial biofilms that extend to normal colon tissue far distant from the tumor. In contrast, biofilm formation is infrequent in colon tumors distal to the hepatic flexure and in the mucosa of colonoscopy controls. Biofilm formation in the human colon is associated with changes in E-cadherin, IL-6 induction, activation of pStat3, colonic epithelial cell proliferation as well as polyamine metabolism. These data suggest biofilm formation promotes pro-carcinogenic immune and epithelial signaling in the human colon. We have further tested our hypothesis that biofilm formation contributes to colon carcinogenesis by examining surgically-removed colons from individuals with Familial Adenomatous Polyposis (FAP) who are destined, as Apc+/- heterozygotes, to develop colon cancer. In contrast to sporadic CRC, early stage FAP patients display patchy biofilm formation throughout the colon and the bacterial composition of FAP-associated colon biofilms differs. Murine studies support synergistic induction of colon tumor formation by select biofilm bacterial members. Together our studies provide additional support for the hypothesis that the microbiota and, specifically, biofilms are an environmental contributor to CRC pathogenesis.

Citation Format: Cynthia L. Sears. The carcinogenic potential of bacterial biofilms. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr IA04.