bluuebunny/crossref_metadata_2025_split huggingface dataset:
SAMMI: a semi-automated tool for the visualization of metabolic networks
Authors: Schultz Andre , Akbani Rehan 
Published: December 2019

Abstract

Summary
Here we present a browser-based Semi-Automated Metabolic Map Illustrator (SAMMI) for the visualization of metabolic networks. While automated features allow for easy network partitioning, navigation, and node positioning, SAMMI also offers a wide array of manual map editing features. This combination allows for fast, context-specific visualization of metabolic networks as well as the development of standardized, large-scale, visually appealing maps. The implementation of SAMMI with popular constraint-based modeling toolboxes also allows for effortless visualization of simulation results of genome-scale metabolic models.

Availability and implementation
SAMMI has been implemented as a standalone web-based tool and as plug-ins for the COBRA and COBRApy toolboxes. SAMMI and its COBRA plugins are available under the GPL 3.0 license and are available along with documentation, tutorials, and source code at www.SammiTool.com.

Supplementary information
Supplementary data are available at Bioinformatics online.
Diagnosis and management of cold urticaria in cryoablation of atrial fibrillation: a case report
Authors: Cordes Friederike , Ellermann Christian , Ehrchen Jan , Ullerich Hansjoerg , Eckardt Lars 
Published: December 2019

Abstract

Background
Cold-induced urticaria is triggered by exposure to local or environmental cold and manifests as localized or systemic pruritic papules, sometimes accompanied by angio-oedema and anaphylaxis representing a life-threatening condition. Therapy options of atrial fibrillation (AF) include catheter ablation with different energy sources, of which cryoenergy may be superior to other energy sources regarding safety and efficacy.

Case summary
We report the case of a 60-year-old man suffering from symptomatic paroxysmal AF. The patient had a history of cold-induced urticaria without occurrence of systemic reactions to date. After successful pulmonary vein isolation (PVI) using cryoenergy, post-interventional oesophagogastroduodenoscopy and endosonography revealed newly occurred oedema in the middle oesophagus with inclusion of all oesophageal wall layers. Due to missing peri-atrial lesions, activation of cold urticaria during cryoablation rather than procedure-associated alterations was diagnosed. The patient reported no systemic or gastrointestinal symptoms after PVI.

Discussion
We could demonstrate that cold urticaria can manifest as oesophageal angio-oedema in AF patients undergoing cryoablation. Therefore, these patients should be carefully considered for an alternative energy source for PVI or premedication with antihistamines when using cryoenergy.
Image detection method of drill cuttings
Authors: Guo Long , Qian Jing , Si Jiangping , Yao Shuxin 
Published: December 2019

Abstract
With the development of digital core technology, numerical simulation experiments have been used by oilfield geologists and geophysicists in rock physics research. However, conducting numerical experiments, such as fluid mechanic simulations, in uncored parts of wells for unavailable digital models to calculate permeability is still impossible. The algorithm filters a large number of Computed Tomography (CT) scanned cutting images and detects whether they can be used to construct a digital core model. This workflow can be applied when coring fails or is too costly. It also provides as much continuous sample data as possible. Conventional methods of acquiring digital cores require coring after drilling and waiting for several months. The method we present here is the innovation of acquiring digital cores in drilling based on a fast CT scanner for a well site. In the future, obtaining petrophysical parameters in uncored strata may be necessary during drilling time. When sandstone is crushed into debris, most of its matrix grains are usually not destroyed. Instead, they are dispersed in the cuttings as loose sand grains. Some original sandstone grains are well connected by cement, and thus may be kept intact as agglomerated grains. These agglomerated grains are selected by collecting a large number of scanned slices. The artificially broken core samples are used for machine learning, and these training models are subsequently used to determine whether the scanned image can be extracted to unspoiled and cemented grains.
Best practice guidelines for arthroscopic intervention in femoroacetabular impingement syndrome: results from an International Delphi Consensus Project—Phase 1
Authors: Radha Sarkhell , Hutt Jonathan , Lall Ajay , Domb Benjamin , Lynch T Sean , Griffin Damian , Field Richard E , Chuck-Cakic Josip 
Published: December 2019

AbstractArthroscopic procedures to treat hip pathologies such as femoroacetabular impingement (FAI) syndrome are now established in mainstream orthopaedic practice. Surgical techniques, rehabilitation protocols and outcomes are widely published. However, consensus on standards of practice remains to be determined. The International Hip Preservation Society (ISHA) has undertaken a research study to identify current areas of consensus across the global hip preservation community. The study focussed on consensus statements on the operative steps in the arthroscopic treatment of FAI syndrome. The study methodology was an online Delphi consensus method to collect aggregate opinions from hip preservation surgeons worldwide. Phase 1 of the planned three-phase study is presented here—focusing on consensus statements on the operative steps in the arthroscopic treatment of FAI syndrome. Ninety-nine statements achieved &gt;80% consensus from a panel of 165 surgeons from six continents. This study is the first to evaluate global consensus on the arthroscopic treatment of FAI syndrome, as well as highlighting areas of contention and avenues for future research.
Financing Da'esh with Sexual Slavery: A Case Study in Not Gendering Conflict Analysis and Intervention
Authors: Hutchinson Susan 
Published: December 2019

Abstract
It is common for the international community to restrict financial flows to terrorist groups as part of efforts to combat terrorism. However, this strategy was less effective with Da'esh because they were a largely financially self-sustaining organization. Analysis of the caliphate's economy and any external funding streams was not gendered. Had analysts understood Da'esh through a gendered lens they could have identified a route toward restricting income. It was known that approximately 7,000 Yazidi women and girls were held in sexual servitude at the height of the caliphate. Because little to no effort was made to account for these women in the battles for Raqqa or Mosul and military operations did not include freeing such slaves, the Yazidi community was left with no choice but to try to buy back their loved ones. This market in sexual slavery may have injected as much as US$21 million into the Da'esh economy, and buying back the remaining captives could provide Da'esh with up to US$90 million more. Had international security operations accounted for those in captivity and freed them as part of the war against Da'esh, it could have reduced this revenue stream. This article calculates the monetary value of Da'esh's market in sexual slavery as a means of demonstrating the effect of not gendering conflict analysis and intervention in the war against Da'esh.
SS1-KL-1 APPLICATION OF AI TECHNOLOGIES FOR MEDICAL CARE
Authors: Hamamoto Ryuji 
Published: December 2019

Abstract
On the basis of progress of the Machine Learning algorithm mainly on the Deep Learning, improvement of the GPU performance, the large-scale public database such as TCGA is available, big attention recently gathers in the AI technology. While large countries such as the United States or China vigorously promote AI research and development by a national policy, Cabinet Office, Government of Japan, also emphasized the importance of AI technologies in the 5th Science and Technology Basic Plan in 2016. As for the AI development, it is wrestled relatively for a long time; the word “Artificial Intelligence” was firstly used in the Dartmouth workshop in 1956. However, the AI development has not been promoted smoothly until now and repeats the active state period and the period of depression. As the current active state period of AI is called as the third AI boom, the most different point of this boom and the other booms is that AI technologies have already been involved in our social life such as the AI-based face authentication device in this period. Indeed, The US Food and Drug Administration (FDA) has already authorized around 30 AI-based medical instruments, and the Pharmaceuticals and Medical Devices Agency (PMDA) in Japan also authorized the first AI-based medical instrument last year. Therefore, now is the important time that we need to consider deeply for the creation of an affluent society, which enables coexistence of human being and AI. In this lecture, I particularly focus on medical imaging analysis using AI technologies and, would like to lecture on an action to the medical care application of the AI technology based on the experience that promoted medical AI research as the leader of two national projects relevant to medical AI called CREST and PRISM, and RIKEN AIP center.
SL2 ADVANCES IN MOLECULAR BIOLOGY AND GENETICS IN GLIOMA RESEARCH AND THERAPY
Authors: Cavenee Webster K 
Published: December 2019

Abstract
The most recent version of the WHO Classification of Tumours of the Central Nervous System includes, for the first time, the joint consideration of tumor pathology with tumor genetics as measured in various ways. This has come decades after the first recognition of genetic lesions in tumor genomes as discerned by cytogenetics and more than 30 years after the first reports of specific and recurrent genetic abnormalities in human tumors, particularly gliomas. This information is vitally important because it is now being used not just for tumor diagnosis but also to indicate specific therapies. In this lecture, I will review the increasingly precise methodologies being employed, the resultant genetic lesions being uncovered and the increasing import of such information for therapeutic selection.
MS3-1 IMPLEMENTATION OF GENE PANEL TESTING USING NEXT-GENERATION SEQUENCING
Authors: Sakai Kazuko 
Published: December 2019

Abstract
The advance of next-generation sequencers (NGS) has dramatically improved the performance of genomic analysis of clinical samples in cancer precision medicine. The practical use of gene panel testing for clinical applications has begun in Japan. At present, “OncomineTM Dx Target Test” is listed as a companion diagnostic system using NGS, and “FoundationOne CDx Cancer Genomic Profile” and “OncoGuide™ NCC Oncopanel System” are listed as gene panel testing under insurance coverage. Formalin-fixed paraffin-embedded specimen have been routinely used for molecular diagnosis testing, therefore quality control such as formalin fixation time and tumor contents is important to ensure validity of diagnostic results. In this presentation, the issue to obtain evaluable results of gene panel testing using formalin-fixed paraffin-embedded specimen will be discussed.
Due to evolution of detection technologies, we can detect gene mutation with high sensitivity. Detection of gene mutation in circulating tumor DNA is feasible approach for diagnostic testing in cancer treatment. Liquid biopsy has been approved as a companion diagnostic testing to detect EGFR mutations in NSCLC. Examples of the clinical utility of plasma testing in cancer treatment will be presented.
S4-KL-1 UPDATE OF WHO2016 CLASSIFICATION OF ADULT DIFFUSE GLIOMAS
Authors: Komori Takashi 
Published: December 2019

Abstract
The World Health Organization (WHO) central nervous system (CNS) tumor classification has represented the primary source of diagnosis and grading criteria of brain tumors. Nonetheless, recent advances of studies on their molecular alterations require more rapid update of recommendations for clinical practice. To accomplish this, cIMPACT-NOW (the Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy) was established in 2016 and has published four updates. For adult gliomas, update 1 clarified the use of the term NOS (Not Otherwise Specified) and proposed a new term NEC (Not Elsewhere Classified); update 2 revised clarifications regarding diffuse astrocytoma/anaplastic astrocytoma, IDH-mutant; update 3 proposed molecular criteria for an IDH-wildtype diffuse or anaplastic astrocytic glioma without histological features of glioblastoma, which would behave similarly to a grade IV glioblastoma. Nonetheless, no consensus on pathologic or molecular markers that could be incorporated into a more clinically relevant grading scheme for IDH-mutant gliomas has been reached. The molecular alterations previously studied using relatively large cohorts include CDKN2A/B homozygous deletion, CDK4 amplification, RB1 mutation/homozygous deletion, PIK3CA or PIK3R1 mutations, PDGFRA amplification, NMYC amplification, global hypomethylation, genomic instability and chromosome 14 loss. The proliferative activity, based on the mitotic count or Ki67 indices, and other morphologic features typical of a high grade that might stratify the risk better than the current criteria have also been evaluated. Despite the discordance among the results of previous studies, CDKN2A/2B homozygous deletions have been shown prognostic significance in high-grade IDH-mutant astrocytomas and microvascular proliferation stratifies IDH-mutant gliomas lacking a CDKN2A homozygous deletion, suggesting that the integration of molecular information and traditional histological findings is still essential for achieving maximum risk stratification of adult cases of IDH-mutant diffuse gliomas. The grading scheme for adult IDH-mutant as well as wild-type gliomas should therefore be revised in the next WHO update.
CBMS-04 SIGNIFICANT ROLE OF HYPOXIA IN THE EXPRESSION AND FUNCTION OF OSTEOPONTIN IN CD44-HIGHLY EXPRESSED GLIOMA STEM-LIKE CELLS IN TUMOR PROGRESSION OF GLIOBLASTOMA
Authors: Nishikawa Masahiro , Inoue Akihiro , Ohtsuka Yoshihiro , Ozaki Saya , Matsumoto Shirabe , Suehiro Satoshi , Yano Hajime , Kanemura Yonehiro , Tanaka Junya , Ohnishi Takanori , Kunieda Takeharu 
Published: December 2019

Abstract
The poor prognosis of glioblastoma multiforme (GBM) may be due to the surviving glioma stem-like cells (GSCs) in the tumor periphery after tumor resection. We demonstrated that CD44-expressed GSCs existed much more in the tumor periphery of high invasive (HI) type GBM than low invasive (LI) type GBM. The HI type was significantly associated with worse outcome, but how GSCs with high CD44 expression relate to tumor progression remains unknown. In this study, we investigated effects of hypoxia on CD44-directed signal pathways, leading to tumor invasion and proliferation in GBM. We focused on the CD44 ligand osteopontin (OPN) because it is known hypoxia affects the interaction of CD44 and OPN which promotes stemness and proliferation of cancer stem cells. We examined mRNA expressions of hypoxia inducible factor (HIF)-1a, HIF-2a, CD44 and OPN in tumor tissues of GBM and investigated effects of hypoxia (1%O2:severe or 5%O2:moderate) on the expression of these molecules using cultured GSCs that were established from tumor tissues showing high CD44 expression in the periphery of GBMs. In addition, we analyzed the effects of OPN on invasive, migratory and proliferative activities of GSCs under the hypoxic conditions. OPN was much higher expressed in the tumor periphery of LI type GBM than HI type GBM. Severe hypoxia significantly increased the expressions of HIF-1a and CD44 but did not OPN. On the other hands, moderate hypoxia promoted the expressions of HIF-2a and OPN. Knockdown of HIF-2a significantly inhibited OPN expression. In addition, the more OPN was expressed in the cultured GSCs under moderate hypoxia, the more the GSCs proliferated and decreased their invasive and migratory activities. In conclusion, GSCs existing in the tumor periphery of GBM can migrate or proliferate by changing CD44-directed signal pathways. Moderate hypoxia promoted HIF-2a/OPN/CD44 pathway, resulting in phenotypic transition to high proliferative tumors.
SPDR-06 PROTEIN DEUBIQUITINATION PATHWAY IS A NOVEL THERAPEUTIC TARGET AGAINST MALIGNANT CNS NON-GERMINOMATOUS GERM CELL TUMORS
Authors: Tomiyama Arata , Uchida Eita , Kobayashi Tatsuya , Wada Kojiro , Ichimura Kouichi 
Published: December 2019

Abstract
Central nervous system germ cell tumors (CNSGCTs) are rare intracranial neoplasm usually developed in adolescents and young adults. However, in East Asia including Japan, incidence of CNSGCTs is considerably higher compare with other regions of the world. Whereas germinomas generally respond to chemo-radiotherapy well, malignant subtypes of non-germinomatous germ cell tumors (NGGCT) are refractory, and development of novel therapy against NGGCTs is urgently needed. To develop a new therapeutic strategy against aggressive NGGCTs, we have investigated novel molecular targets for NGGCT treatment. We screened a total of 120 CNSGCT tumor tissues (including 55 NGGCT), which were registered to the Intracranial Germ Cell Tumor Consortium (iGCT), and discovered multiple mutations of a molecule that regulates protein ubiquitination and degradation specifically in NGGCT cases (5 of 55 cases; 1 immature teratoma, 3 mixed gem cell tumors, and 1 embryonal carcinoma). An in vitro ubiquitination assay revealed the mutations of this molecule discovered in NGGCT cases were loss of function mutations. Reduced expression of this molecule by knockdown in an established human seminoma cell line Tcam2 or a human yolk sac tumor cell line YST1, which was recently established in our institute, resulted in enhanced proliferation as well as upregulation of MEK-ERK activation. Importantly, treatment of these two GCT cell lines with reduced expression of this molecule by MEK inhibitor trametinib suppressed augmented proliferation of these cells. Taken together, these results suggest that protein ubiquitination-related pathways as well as MEK-ERK cascade may serve as a novel therapeutic target against NGGCTs.
ET-02 EFFICACY OF THE SALVAGE THERAPY VIA LOMUSTINE AND NIMUSTINE FOR RECURRENT GLIOBLASTOMA WITH TEMOZOLOMIDE RESISTANCE
Authors: Yamamuro Shun , Ichimura Koichi , Takahashi Masamichi , Tomiyama Arata 
Published: December 2019

Abstract
Temozolomide (TMZ) is widely used as a part of the standard treatment of glioblastomas (GBMs). However, GBM often acquires resistance for TMZ after continuous treatment with TMZ and recurs as TMZ resistance GBM (TMZ-R GBM). Other alkylating agents such as lomustine (CCNU) or nimustine (ACNU) have been sometimes used as a salvage therapy for those TMZ-R GBMs, however, their efficacy against TMZ-R GBMs has not been thoroughly investigated yet. In this study, we investigated anti-tumor effects of CCNU and ACNU for TMZ-R GBM cell lines in vitro to examine whether these agents could become alternative to TMZ in the therapy of TMZ-R GBMs. TMZ resistant clones of human GBM cell lines U87 MG (U87-R cells) and U251 MG (U251-R cells) were established as the TMZ-R GBM cell lines by cultivating U87 MG cells and U251 MG cells under continuous TMZ treatment for at least 1 year. Induction of growth arrest and apoptosis by TMZ, CCNU or ACNU against these cells were analyzed by dye exclusion assay, vital dye staining assay, and immunoblotting. The results showed that growth arrest and apoptosis were triggered upon these cells after administration of each drugs. As expected, the anti-tumor effects of TMZ for U87-R cells or U251-R cells were significantly reduced compared with those for parental U87 MG cells or U251 MG cells, respectively. On the other hand, CCNU and ACNU showed similar growth suppressive effect upon U87-R cells or U251-R cells as compared with U87 MG cells or U251 MG cells. Throughout these experiments, CCNU demonstrated strongest anti-tumor effects for all cell lines, both parental and TMZ-R GBM cell lines, and ACNU also demonstrated stronger effects than TMZ. These results suggest that CCNU or ACNU may serve as a drug of choice for salvage treatment of TMZ-R GBM.
TB-03 THE SURVIVAL PROLONGATION EFFECT OF NOVEL BORON COMPOUND FOR BNCT USING RAT BRAIN TUMOR MODEL
Authors: Fukuo Yusuke , Kawabata Shinji , Kashiwagi Hideki , Kanemitsu Takuya , Takeuchi Kouji , Hiramatsu Ryo , Wanibuchi Masahiko , Ono Kouji , Miyatake Shinichi 
Published: December 2019

Abstract

INTRODUCTION
Boron neutron capture therapy (BNCT) is form of tumor-cell selective particle irradiation. Although novel boron compounds have been developed, BPA (boronophenylalanine) and BSH (borocaptate sodium) are used in the clinical practice. The development of effective boron compounds is a major theme. We used Dodecaborate-containing BPA (AAL) which is combined the characteristics of both BPA and BSH. We have been conducting research on how the new compound for BNCT will affect rat brain tumor model.

MATERIALS AND METHODS
We evaluated the boron concentration of F98 glioma cells for BPA and AAL, and the biodistribution of these following BPA administrated intravenously (i.v.) or AAL administrated by convection-enhanced delivery (CED) in F98 glioma bearing rats. In BNCT study, the therapeutic effect was evaluated in terms of the survival time for all rats divided into six groups.

RESULTS
The uptake of boron showed almost the same value at all exposure times in high concentration. In biodistribution study, the AAL(CED) 6h after the termination group attained the highest boron concentrations of the tumor (59.9 ± 18.2 μg/g). In the BNCT study, the median survival time in the AAL(CED) group (31(29–35) days) was shorter than that in the BPA(i.v.) group(34(33–36) days). And the combination group of AAL(CED) and BPA(i.v.) gave the most significant prolongation of survival(38(36–40) days).

DISCUSSION
AAL(CED) and BPA(i.v.) combined group had a significant survival prolongation compared with the single-agent group. It is thought that AAL irradiated by thermal neutron had a cell-killing effect on cells in which BPA was not taken up. The combination uses of AAL (CED) provides additional BNCT effects. The mechanism by which AAL is incorporated has not been clarified, and further experiments including the influence on normal cells are in progress.

CONCLUSION
Dodecaborate-containing BPA (AAL) is a novel boron compound for BNCT that can be expected to prolong the survival time in combination with BPA.