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Supplementary materials and methods

IL-34 expression in cancers

Correlation between IL-34 and clinic-pathological characteristics, and Cox's proportional hazards model analysis of prognostic factors for OS in NSCLC patients

The ability of tumor cells to escape immune destruction and their acquired resistance to chemotherapy are major obstacles to effective cancer therapy. Although immune checkpoint therapies such as anti-PD-1 address these issues in part, clinical responses remain limited to a subpopulation of patients. In this report, we identified IL34 produced by cancer cells as a driver of chemoresistance. In particular, we found that IL34 modulated the functions of tumor-associated macrophages to enhance local immunosuppression and to promote the survival of chemoresistant cancer cells by activating AKT signaling. Targeting IL34 in chemoresistant tumors resulted in a remarkable inhibition of tumor growth when accompanied with chemotherapy. Our results define a pathogenic role for IL34 in mediating immunosuppression and chemoresistance and identify it as a tractable target for anticancer therapy. Cancer Res; 76(20); 6030–42. ©2016 AACR.

Gemcitabine amplifies the expression of multiple MDSCs-inducing cytokines including GM-CSF in PANC-1 cell line.

Supplementary Table A. Association between GM-CSF and clinicopathological variables Supplementary Table B. Clinicopathological features of enrolled PDAC patients with or without chemotherapy Supplementary Table C. Clinicopathological features including drug regimen or chemotherapeutic response of enrolled 6 PDAC patients with pre-operative chemotherapy.

No significant difference in the frequencies of CD68+ macrophages in cancer patients after treatment with pre-operative chemotherapy.

Supplemental Figure Legends

Blockade of GM-CSF contributes to the recovery of CD8+ T cells proliferation when cultured with monocytes stimulated with chemotherapy-treated PDAC CM.

5-FU-treated Capan-1 supernatants induce the differentiation of monocytes into MDSCs.

Gemcitabine amplifies the expression of IL-6 or IL8 in Capan-1 cells.

Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic malignancies. PDAC builds a tumor microenvironment that plays critical roles in tumor progression and metastasis. However, the relationship between chemotherapy and modulation of PDAC-induced tumor microenvironment remains poorly understood. In this study, we report a role of chemotherapy-derived inflammatory response in the enrichment of PDAC microenvironment with immunosuppressive myeloid cells. Granulocyte macrophage colony-stimulating factor (GM-CSF) is a major cytokine associated with oncogenic KRAS in PDAC cells. GM-CSF production was significantly enhanced in various PDAC cell lines or PDAC tumor tissues from patients after treatment with chemotherapy, which induced the differentiation of monocytes into myeloid-derived suppressor cells (MDSC). Furthermore, blockade of GM-CSF with monoclonal antibodies helped to restore T-cell proliferation when cocultured with monocytes stimulated with tumor supernatants. GM-CSF expression was also observed in primary tumors and correlated with poor prognosis in PDAC patients. Together, these results describe a role of GM-CSF in the modification of chemotherapy-treated PDAC microenvironment and suggest that the targeting of GM-CSF may benefit PDAC patients' refractory to current anticancer regimens by defeating MDSC-mediated immune escape. Cancer Res; 75(13); 2629–40. ©2015 AACR.

Popular data concentration is a widely accepted storage energy-saving technique which places frequently-accessed data on a small subset of hard disks and spins-down other infrequently-accessed disks. Many previous studies use intuitive heuristic algorithms for data placement that promote the imbalance in the access frequencies across hard disks. However, the relevance and the optimality of such file placements have not been rigorously investigated. In this paper, we formally define the energy-saving file placement problem under the capacity and performance constraints as a combinatorial optimization problem and show the theory of the optimal file placement where the file access rates in the next period are given. Our analysis based on a stochastic process of disk state transitions gives the theoretical support for the common heuristic placement method. To examine the effectiveness of the optimal file placement, we experimentally evaluate the energy-efficiency of a test storage system using the file access rates generated from the real access traces from Flickr. The experimental results show that the energy consumption can be reduced by 31.8% with the optimal file placement compared to the evenly distributed file placement. We also conduct simulation experiments to confirm the energy-saving impacts in larger-scale storage systems.

Big-data processing systems such as Hadoop, which usually utilize distributed file systems (DFSs), require data reduction schemes to maximize storage space efficiency. These schemes have different tradeoffs, and there are no all-purpose schemes applicable to all data. Users must select a suitable scheme in accordance with their data. To accommodate this requirement, application software or file system (FS) have a fixed selection of these schemes. However, these provided schemes are insufficient for all data types, and when novel schemes emerge, extending the selection can be problematic. If the source code of the application or FS is available, the source code could potentially be extended with extensive labor, but could be virtually impossible without the code maintainers’ assistance. If the source code is unavailable, there is no way to tackle the problem. This paper proposes an unexplored solution through a modular DFS design that eases data reduction scheme usage through existing programming techniques. The advantages of this presented approach are threefold. First, adding new schemes is easy and they are transparent to the application code requiring no extensions to it. Second, the modular structure requires minimal modification to the existing DFSs and performance overhead. Third, users can compile schemes separately from the DFS without the FS or DFS source code. To demonstrate the design’s effectiveness, we implemented it by minimally extending the Hadoop DFS (HDFS) and named it the Hadoop Data Reduction Framework (HDRF). We designed HDRF to work with minimal overhead and tested it extensively. Experimental results indicate that it has negligible overhead over existing approaches. In a number of cases, it can offer up to 48.96% higher throughput while achieving the best result in storage reduction within our tested setups because of the incorporated data reduction schemes.

Highlights • Thymic basaloid carcinoma is one of the rarest subtypes of thymic carcinoma. • To our knowledge, this is the first case report of thymic basaloid carcinoma concurrent another carcinoma. • Aggressive treatment including surgery should be considered aiming at radical cure., Introduction Thymic basaloid carcinoma is rare, as only about 40 reports have described it since the initial report. Thymoma and thymic carcinomas increase the risk of other malignancies, but concurrent thymic basaloid carcinoma and another malignancy has not been reported. We presented a rare case of thymic basaloid carcinoma with rectal carcinoma. Case presentation Computed tomography revealed an anterior mediastinal mass and rectal wall thickening, and colonoscopy identified a rectal type 2 tumor in a 68-year-old man. Total thymectomy via a median sternotomy was performed, and the thymic tumor was histopathologically confirmed as stage II thymic basaloid carcinoma. Subsequent laparoscopic low anterior resection indicated stage IIIa rectal carcinoma. Adjuvant chemotherapy was administered for the rectal cancer. Discussion Concurrent thymic and extrathymic tumors is rare condition. There are few reports of thymic basaloid carcinoma, and it is unclear whether this tumor, like common thymoma, increase the risk of extrathymic malignancies. Further studies in more patients are needed to elucidate the nature of this tumor. Conclusion To our knowledge, this is the first case report of thymic basaloid carcinoma concurrent another carcinoma. Aggressive treatment including surgery should be considered aiming at radical cure.

Multi-path TCP (MPTCP) is a network protocol that has the potential to enhance network performance, which is crucial in grid computing systems to improve the overall system's performance. It utilizes multiple network paths between machines to achieve a high network performance. This protocol can also improve the connectivity of multiple servers that may be in different data centers by combining multiple network paths. One of the main issues of MPTCP is the path for ACK (acknowledgment) packets, which take the same path where original packets come from. When networks have different round trip times (RTTs), MPTCP may dispatch the ACK packet through a longer path, which is inefficient. HayACK solves this issue by selecting the path with the least RTTs. However, HayACK may suffer from inconsistent packets because of middleboxes, which are intermediary devices between the source and the destination that process network packets. These middleboxes may discard MPTCP packets because of inconsistent sequence numbers of HayACK packets, which is a product of HayACK's path selection. This study aims to investigate the usefulness of HayACK for high-performance data transfer when using multiple paths in real network environments and the influence of middleboxes on HayACK. Our investigation was conducted using various network paths by preparing many client hosts with different IP addresses and one server. The influence of middleboxes is determined by checking the probe packets passed through, changed, or discarded. Assuming the HayACK response, we crafted packets such as TCP SYN packets and TCP ACK packets.

// Shoki Sato 1 , Toru Nakamura 1 , Toyomasa Katagiri 2 , Takahiro Tsuchikawa 1 , Toshihiro Kushibiki 1 , Kouji Hontani 1 , Mizuna Takahashi 1 , Kazuho Inoko 1 , Hironobu Takano 1 , Hirotake Abe 1 , Shintaro Takeuchi 1 , Masato Ono 1 , Shota Kuwabara 1 , Kazufumi Umemoto 1 , Tomohiro Suzuki 1 , Osamu Sato 1 , Yusuke Nakamura 3 and Satoshi Hirano 1 1 Department of Gastroenterological Surgery II, Hokkaido University Graduate School of Medicine, Sapporo, Japan 2 Division of Genome Medicine, Institute for Genome Research, Tokushima University, Tokushima, Japan 3 Department of Medicine and Surgery, The University of Chicago, Chicago, IL, USA Correspondence to: Toru Nakamura, email: torunakamura@med.hokudai.ac.jp Keywords: C16orf74; pancreatic ductal adenocarcinoma; cell-permeable peptide; molecular target therapy Received: May 04, 2017 Accepted: July 26, 2017 Published: October 19, 2017 ABSTRACT Background: Chromosome 16 open reading frame 74 ( C16orf74 ) is highly expressed in pancreatic ductal adenocarcinoma (PDAC) and is involved in cancer cell proliferation and invasion through binding to calcineurin (CN). Therefore, C16orf74 is a good target for the development of a PDAC treatment. A cell-permeable dominant-negative (DN) peptide that can inhibit the C16orf74/CN interaction was designed to examine whether this peptide can inhibit PDAC cell proliferation in vitro and in vivo . Method: TheDN-C16orf74 peptide, which corresponds to the portion of C16orf74 that interacts with CN, was synthesized, and we assessed its anti-tumor activity in proliferation assays with human PDAC cells and the underlying molecular signaling pathway. Using an orthotopic xenograft model of PDAC, we treated mice intraperitoneally with phosphate-buffered saline (PBS), control peptide, or DN-C16orf74 and analyzed the tumor-suppressive effects. Result: DN-C16orf74 inhibited the binding of C16orf74 to CN in an immunoprecipitation assay. DN-C16orf74 suppressed PDAC cell proliferation, and the level of suppression depended on the expression levels of C16orf74 in vitro . DN-C16orf74 also exhibited anti-tumor effects in orthotopic xenograft model. Furthermore, the tumor-suppressive effect was associated with inhibition of the phosphorylation of Akt and mTOR. Conclusion: The cell-permeable peptide DN-C16orf74 has a strong anti-tumor effect against PDAC in vitro and in vivo .

To empower scientists who are engaged in nation-wide or global-scale collaborative projects for scientific discovery, a large amount of scientific data needs to be visualized and then shared among the scientists. Tiled Display Wall?(TDW) has been widely accepted and used for visualization of large-scale scientific data. Scalable Adaptive Graphics Environment?(SAGE) has received attention from scientists as a middleware that organizes multiple display monitors into a network-aware large display monitor. Using a SAGE TDW, scientists can display multiple visualized contents on a single display monitor, each of which can be located at geographically distant site managed by other organizations. However, SAGE does not have a mechanism for managing multiple visualized data streams heading to a single TDW. In a conventional network, data flows for a same destination tend to share a same link, resulting in drop of packets and therefore poor visual quality. Moreover, because of the flexible nature of SAGE, rate of each visual data flow may change dynamically as a result of user interaction on a TDW, such as moving and resizing an application window. For the reason above, we propose and develop a dynamic route allocation method that switches packet flows onto network links where better performance is expected, in response to user interaction such as window movement and resizing. Technically, we have leveraged OpenFlow, an implementation of Software Defined Networking?(SDN), to integrate network programmability into SAGE. In this paper, we show how SAGE enhanced with the proposed method succeeded in avoiding network congestion and improving the quality of visualization on the TDW over the wide area OpenFlow network on the Internet. SAGE is a TDW middleware that can receive multiple streams from multi site.Dynamic changes of network traffic caused by user-interaction in SAGE.We modified SAGE with dynamic routing functionality triggered by user interaction.Dynamic routing functionality is implemented using OpenFlow.It aims to avoid network congestion for keeping high quality visualization.

Ephrin receptor A4 (EphA4) is overexpressed in human pancreatic adenocarcinoma (PDAC) and activate cell growth. Recent studies have identified small molecules that block EphA4. In this study, we investigated the correlation between EphA4 expression and the prognosis of patients with PDAC. We also examined the cytostatic efficacy of 2,5-dimethylpyrrolyl benzoic acid (compound 1), a small molecule that blocks EphA4, in PDAC cells. Overall survival of patients with EphA4 positivity was significantly shorter than that of patients with EphA4 negativity (P = 0.029). In addition, multivariate analysis revealed that EphA4 expression was an independent prognostic factor in PDAC patients (P = 0.039). Compound 1 showed a cytostatic efficacy in PDAC cells expressing EphA4 in vitro and in vivo. Our study indicated that compound 1 suppressed both EphA4 and Akt phosphorylations, and induced apoptosis in PDAC cells expressing EphA4. In conclusion, compound 1 has a high potential as a therapeutic agent for patients with PDAC.

Supplementary data for this article are available at Cancer Research Online, Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic malignancies. PDAC builds a tumor microenvironment that plays critical roles in tumor progression and metastasis. However, the relationship between chemotherapy and modulation of PDAC-induced tumor microenvironment remains poorly understood. In this study, we report a role of chemotherapy-derived inflammatory response in the enrichment of PDAC microenvironment with immunosuppressive myeloid cells. Granulocyte macrophage colony-stimulating factor (GM-CSF) is a major cytokine associated with oncogenic KRAS in PDAC cells. GM-CSF production was significantly enhanced in various PDAC cell lines or PDAC tumor tissues from patients after treatment with chemotherapy, which induced the differentiation of monocytes into myeloid-derived suppressor cells (MDSC). Furthermore, blockade of GM-CSF with monoclonal antibodies helped to restore T-cell proliferation when cocultured with monocytes stimulated with tumor supernatants. GM-CSF expression was also observed in primary tumors and correlated with poor prognosis in PDAC patients. Together, these results describe a role of GM-CSF in the modification of chemotherapy-treated PDAC microenvironment and suggest that the targeting of GM-CSF may benefit PDAC patients' refractory to current anticancer regimens by defeating MDSC-mediated immune escape., http://cancerres.aacrjournals.org/content/75/13/2629.figures-only

The ability of tumor cells to escape immune destruction and their acquired resistance to chemotherapy are major obstacles to effective cancer therapy. Although immune checkpoint therapies such as anti-PD-1 address these issues in part, clinical responses remain limited to a subpopulation of patients. In this report, we identified IL34 produced by cancer cells as a driver of chemoresistance. In particular, we found that IL34 modulated the functions of tumor-associated macrophages to enhance local immunosuppression and to promote the survival of chemoresistant cancer cells by activating AKT signaling. Targeting IL34 in chemoresistant tumors resulted in a remarkable inhibition of tumor growth when accompanied with chemotherapy. Our results define a pathogenic role for IL34 in mediating immunosuppression and chemoresistance and identify it as a tractable target for anticancer therapy. Cancer Res; 76(20); 6030–42. ©2016 AACR.

In this paper, we propose a method for the dynamic migration of the IP routing points using binary particle swarm optimization (PSO) in distributed Virtual LAN environments. Virtual LAN (VLAN) is a virtualization technique of datalink layer and can construct arbitrary logical networks on top of a physical network. However, VLAN often causes much redundant traffic due to mismatch between the topology of the logical network and that of the underlying physical network. We will show that the proposed method can adaptively select the routing points dynamically according to the observed traffic patterns and thus reduce the redundant traffic. Finally, we will evaluate the proposed method using the simulation environment.

Network testbeds have been used for network measurement and experiments. In such testbeds, resources, such as CPU, memory, and I/O interfaces, are shared and virtualized to maximize node utility for many users. A few studies have investigated the impact of virtualization on precise network measurement and understood Internet traffic characteristics on virtualized testbeds. Although scheduling latency and heavy loads are reportedly affected in precise network measurement, no clear conditions or criteria have been established. Moreover, empirical-statistical criteria and methods that pick out anomalous cases for precise network experiments are required on userland because virtualization technology used in the provided testbeds is hardly replaceable. In this paper, we show that ‘oversize packet spacing’, which can be caused by CPU scheduling latency, is a major cause of throughput instability on a virtualized network testbed even when no significant changes occur in well-known network metrics. These are unusual anomalies on virtualized network environment. Empirical-statistical analysis results accord with results at previous work. If network throughput is decreased by the anomalies, we should carefully review measurement results. Our empirical approach enables anomalous cases to be identified. We present CPU availability as an important criterion for estimating the anomalies.

Cancer vaccines serve as a promising clinical immunotherapeutic strategy that help to trigger an effective and specific antitumor immune response compared to conventional therapies. However, poor immunogenicity of tumor cells remains a major obstacle for clinical application, and developing new methods to modify the immunogenicity of tumor cells may help to improve the clinical outcome of cancer vaccines. 4T1 mouse breast cancer cell line has been known as poorly immunogenic and highly metastatic cell line. Using this model, we identified a sub cell line of 4T1-designated as 4T1-Sapporo (4T1-S)-which shows immunogenic properties when used as a vaccine against the same line. In 4T1-S-vaccinated mice, subcutaneous injection of 4T1-S resulted in an antitumor inflammatory response represented by significant enlargement of draining lymph nodes, accompanied with increased frequencies of activated CD8 T cells and a subpopulation of myeloid cells. Additionally, 4T1-S vaccine was ineffective to induce tumor rejection in nude mice, which importantly indicate that 4T1-S vaccine rely on T cell response to induce tumor rejection. Further analysis to identify mechanisms that control tumor immunogenicity in this model may help to develop new methods for improving the efficacies of clinical cancer vaccines.

Anomaly detection is a promising approach to detecting intruders masquerading as valid users (called masqueraders). It creates a user profile and labels any behavior that deviates from the profile as anomalous. In anomaly detection, a challenging task is modeling a user’s dynamic behavior based on sequential data collected from computer systems. In this paper, we propose a novel method, called Eigen co-occurrence matrix (ECM), that models sequences such as UNIX commands and extracts their principal features. We applied the ECM method to a masquerade detection experiment with data from Schonlau et al. We report the results and compare them with results obtained from several conventional methods.