tbuckley/cabot-search huggingface dataset:
A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes
Authors: Guangwei Li, Lijian Wang, Jianping Yang, Hang He, Huaibing Jin, Xuming Li, Tianheng Ren, Zhenglong Ren, Feng Li, Xue Han, Xiaoge Zhao, Lingli Dong, Yiwen Li, Zhongping Song, Zehong Yan, Nannan Zheng, Cuilan Shi, Zhaohui Wang, Shuling Yang, Zijun Xiong, Menglan Zhang, Guanghua Sun, Xu Zheng, Mingyue Gou, Changmian Ji, Junkai Du, Hongkun Zheng, Jaroslav Doležel, Xing Wang Deng, Nils Stein, Qinghua Yang, Kunpu Zhang, Daowen Wang
Journal: Nature Genetics (2021)

Abstract Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela , Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.
HSR21-057: Cost-Effectiveness of Cemiplimab vs Pembrolizumab for the First-Line Treatment of Patients With Advanced Non-Small Cell Lung Cancer (aNSCLC) and Programmed Death-Ligand 1 (PD-L1) Expression ≥50% in the US
Authors: Andreas Kuznik, Meena Venkatachalam, Gerasimos Konidaris, Chieh-I Chen, Sam Keeping, Kokuvi Atsou, Yingxin Xu, Florence Wilson, Patricia Guyot, Keith Chan, Emily Glowienka, Caitlin Smare
Journal: Journal of the National Comprehensive Cancer Network (2021)

"HSR21-057: Cost-Effectiveness of Cemiplimab vs Pembrolizumab for the First-Line Treatment of Patients With Advanced Non-Small Cell Lung Cancer (aNSCLC) and Programmed Death-Ligand 1 (PD-L1) Expression ≥50% in the US" published on 17 Mar 2021 by National Comprehensive Cancer Network.
Novel lung cancer cell lines, Ma44-3L and Ma44-3M established by in vivo selection reveal candidate genes for lymph node metastasis
Authors: Hiromitsu Takizawa, Kazuya Kondo, Haruhiko Fujino, Takanori Miyoshi, Koichiro Kenzaki, Shoji Sakiyama, Akira Tangoku
Journal: Cancer Research (2008)

390  Lymphogenous spread is the first step of tumor progression and the extent of lymph node metastasis is a crucial prognostic parameter in patients with lung cancer. To clarify the key genes that are concerned in lymph node metastasis of lung cancer, we established two cell lines which metastasize to mediastinal lymph node in high and low frequency from a parental lung cancer cell line by in vivo selection and performed cDNA microarray analysis of these cell lines. In our previous experiment, after Ma44-3, lung cancer cell line, were orthotopically implanted to severe combined immunodeficiency (SCID) mice, macroscopically detectable tumor was formed at the site of injection on day 9 and mediastinal lymph node metastasis was observed on day 12. Using this model, lung tumors were harvested for culturing and implanted to the next generation mice. In the same way, metastatic mediastinal lymph nodes were passaged. These two passages were repeated five times. We established Ma44-3L from the lung tumor passage and Ma-44M from the mediastinal lymph node passage. These isolated cells were orthotopically implanted to each by five SCID mice to evaluate the potential of metastasis. The mice were sacrificed 2 weeks after implantation. Maximal diameter of the lung tumors and presence of mediastinal lymph node metastasis were evaluated. These two cell lines were subjected to cDNA microarray analysis followed by data mining studies. The lung tumors of Ma44-3L were significantly larger than that of Ma44-3M (3.28 ± 1.12 mm versus 1.74 ± 0.62 mm, p = 0.03). Ma44-3M metastasized to mediastinal lymph node in high frequency compared with Ma44-3L (5/5 versus 1/5, p = 0.01). We identified 79 genes that were 6-fold differentially expressed in Ma44-3L and Ma44-3M by cDNA microarray containing 14551 known genes. Genes upregulated in Ma44-3M cells included thrombospondin 1 and CD33 antigen, etc. that had been previously reported to be associated to metastasis of cancer cells. In conclusion, we established new cell lines with different potential to metastasize to mediastinal lymph node by in vivo selection. The candidate genes listed up by cDNA microarray may include key genes which are associated to important roles in lymph node metastasis in patients with lung cancer.
<i>Aurka</i> loss in CD19<sup>+</sup> B cells promotes megakaryocytopoiesis via IL-6/STAT3 signaling-mediated thrombopoietin production
Authors: Xin Chen, Chennan Wang, Na Sun, Shuai Pan, Rongqing Li, Xueqin Li, Jie Zhao, Huan Tong, Yangyang Tang, Jing Han, Jianlin Qiao, Hongbin Qiu, Hui Wang, Jing Yang, Takayuki Ikezoe
Journal: Theranostics (2021)

Rationale: Aurora kinase A (Aurora-A), which is required for mitosis, is a therapeutic target in various tumors. Targeting Aurora-A led to an increase in the differentiation and polyploidization of megakaryocytes both in vivo and in vitro. However, the mechanisms involved in controlling megakaryocyte differentiation have not been fully elucidated. Methods: Conditional Aurka knockout mice were generated. B cell development, platelet development and function were subsequently examined. Proplatelet formation, in vivo response to mTPO, post-transfusion experiment, colony assay, immunofluorescence staining and quantification, and ChIP assay were conducted to gain insights into the mechanisms of Aurka loss in megakaryocytopoiesis. Results: Loss of Aurka in CD19+ B cells impaired B cell development in association with an increase in the number of platelets in peripheral blood (PB). Surprisingly, thrombopoietin (TPO) production and IL-6 were elevated in the plasma in parallel with an increase in the number of differentiated megakaryocytes in the bone marrow (BM) of Aurkaf/f;Cd19Cre/+ mice. Interestingly, compared with that of the Aurkaf/f mice, a higher number of CD19+ B cells close to megakaryocytes was observed in the BM of the Aurkaf/f;Cd19Cre/+ mice. Moreover, Aurka loss in CD19+ B cells induced signal transducer and activator of transcription-3 (STAT3) activation. Inhibition of STAT3 reduced the Tpo mRNA levels. ChIP assays revealed that STAT3 bound to the TPO promoter. Additionally, STAT3-mediated TPO transcription was an autocrine effect provoked by IL-6, at least partially. Conclusions: Deletion of Aurka in CD19+ B cells led to an increase in IL-6 production, promoting STAT3 activation, which in turn contributed to TPO transcription and megakaryocytopoiesis.
Donanemab in Early Alzheimer’s Disease
Authors: Mark A. Mintun, Albert C. Lo, Cynthia Duggan Evans, Alette M. Wessels, Paul A. Ardayfio, Scott W. Andersen, Sergey Shcherbinin, JonDavid Sparks, John R. Sims, Miroslaw Brys, Liana G. Apostolova, Stephen P. Salloway, Daniel M. Skovronsky
Journal: New England Journal of Medicine (2021)

A hallmark of Alzheimer's disease is the accumulation of amyloid-β (Aβ) peptide. Donanemab, an antibody that targets a modified form of deposited Aβ, is being investigated for the treatment of early Alzheimer's disease.
Abstract 215: Fatal Arrhythmia In The Adult Patient Of Kawasaki Disease
Authors: Hirofumi Watanabe, Mamoru Ayusawa, Hiroshi Kamiyama, Kensuke Karasawa, Syouri Takahashi
Journal: Circulation (2015)

We herein report the two adult patients hardly predictable sudden cardiac arrest caused by presumed Kawasaki disease (KD). Case 1: A 29- year-old man who had a history of KD at 10 months of his age complicated with bilateral giant coronary aneurysms, and was received a surgery of coronary artery bypass grafting (CABG) when he was 17 years old. He was transferred to emergency center because of sudden cardiac arrest during live concert and revived by automated external defibrillator (AED). Case 2: A 26-year-old man with a history of KD at 1year old of his age, complicated with bilateral giant coronary aneurysms, and was received a catheter intervention of rotational atherectomy (ROTA) to left anterior descending (LAD) artery at 16 years old of his age. He suddenly fell with ventricular fibrillation (VF) on playing futsal, and was hospitalized after revival by AED. Both of them had past history of myocardial infarction (MI) in their youths, however, did not have left ventricular dysfunction, symptomatic arrhythmia, and evidence of acute MI at admission. Therefore, it was difficult to strongly predict possibility of fatal arrhythmia in these cases. Finally, they received the second CABG’s for each after stabilizing and returned to their daily lives. It had been rarely reported a fatal arrhythmia in asymptomatic KD patients with normal left ventricular function with revival with recent spread of life support with public access of defibrillator. Our experiences may suggest one style with a paradigm shift in management of patients with coronary artery complications at the remote period of KD.
Successful endoscopic papillectomy with intrapancreatic ductal radiofrequency ablation for ampulla cancer in surgically altered anatomy
Authors: Jung Su Lee, Hoonsub So, Jun Seong Hwang, Sung Woo Ko, Tae Jun Song
Journal: Endoscopy (2021)

Surgical resection of ampullary neoplasms in patients with surgically altered anatomy is challenging [1]. The recent development of intraductal radiofrequency ablation (RFA) devices and endoscopic techniques enabled endoscopic treatments to be used as viable alternatives for ampullary neoplasm in poor surgical candidates [2] [3] [4]. We describe a case of endoscopic papillectomy with intraductal RFA for an ampullary tumor in a patient with Billroth II anastomosis.
Abstract 11288: Discordance Between Immunofluorescence and Immunohistochemistry C4d Staining is a Risk Factor for Adverse Outcomes Post Heart Transplantation
Authors: Takeo Fujino, Yuto Kumai, Benjamin Yang, Sara Kalantari, Jayant Raikhelkar, Kammi Henriksen, Anthony Chang, Aliya N Husain, Gene Kim, Gabriel Sayer, Nir Uriel
Journal: Circulation (2019)

Introduction: Deposition of complement C4d in the myocardium is an important marker of antibody-mediated rejection (AMR) following heart transplantation (HT) and related to worse outcomes. There ar...
MA02.05 NAVIGATE 24-Month Results: Electromagnetic Navigation Bronchoscopy for Pulmonary Lesions at 37 Centers in Europe and the US
Authors: E. Folch, D. Arenberg, S. Bansal, M. Bezzi, K. Bhadra, M. Bowling, M. Christensen, J. Flandes, T. Gildea, K. Hogarth, W. Krimsky, B. Lamprecht, K. Lau, G. Lemense, A. Mahajan, S. Murgu, B. Murillo, M. Nead, M. Pritchett, J. Singh, C. Towe, S. Khandhar
Journal: Journal of Thoracic Oncology (2021)
Do asymptomatic carriers of SARS-COV-2 transmit the virus?
Authors: Claude P. Muller
Journal: The Lancet Regional Health - Europe (2021)

There is a strong coordinated effort by vaccination groups all over the world to put an end to the current crisis of COVID-19. Now sufficient data are available to analyse and compare some results to explore the aftereffects of vaccination. Some influence variables on transmissions of the disease were discussed e.g., mass vaccination, lockdown and seasonality. Most studies covered here are up to the beginning of July 2022, while some analyses focused on the earlier period of mass vaccination. Well established, simple statistical techniques to evaluate results were presented those used open data sources of authoritative bodies. Some comparisons between vaccinated vs. unvaccinated were also discussed based on data from UK Government Health Security Agency (UHSA). In terms of mass vaccination, adverse reactions after vaccination received attention, as health and safety issues of the general public are of prime importance. Apart from direct side effects, the secondary effect of mass vaccination needs attention too. After the initiation of the vaccination programme, almost all countries experienced a sudden surge in transmission and most countries had to impose strict lockdown measures. Many countries, with a low prevalence of disease, suddenly showed a steep jump and some countries even followed a synchronized pattern between the rate of transmissions and the variation of vaccine doses. Time series analyses and bar diagram presentations were able to capture those features. In that context, fast mutation of the virus and new variants after mass vaccination and possible mechanisms/consequences were also attended. To understand the effect of seasonality, similarities between COVID-19 and the seasonal Flu are discussed for Europe and US to gain useful insight. Using time series analyses and spatial plots of regional temperature composites we showed, like Flu, seasonality played a dominant role in transmissions of COVID-19 in the Europe. Regulations of vaccine dose and policy implication were explored too. From 22nd December 2021, global vaccine doses were reduced substantially, which followed a dramatic reduction in cases and thereafter deaths with around one month's lag between each. As strong dependency on seasonality is noticed in certain countries and observing that regulation of vaccine doses has roles in modulating the transmission with certain lags, globally as well as regionally, our results have policy implications for the management of COVID. Debating, questioning and criticism are always the foundation of great science and the major pillars of its progress. Following that objective, it is an effort to explore pragmatically, supported by scientific analyses, areas relating to the effectiveness of the COVID-19 vaccine and the exit strategy via the pathway of vaccination.
P24.04 Outcome of Neoadjuvant or Adjuvant Radiotherapy in Multimodality Setting with EPP for Malignant Pleural Mesothelioma
Authors: A. Hoda, T. Klikovits, K. Sinn, R. Hritcu, B. Mosleh, S. Zoechbauer-Mueller, W. Koestler, G. Lang, K. Hoetzenecker, K. Dieckmann, J. Widder, W. Klepetko
Journal: Journal of Thoracic Oncology (2021)
FP12.06 GRIm-Score Variations Predict Outcome in Metastatic NSCLC Patients Treated with First-Line Pembrolizumab
Authors: E. Lenci, L. Cantini, S. Rinaldi, F. Pecci, V. Cognigni, V. Agostinelli, G. Mentrasti, N. Ranallo, A. Lupi, F. Paoloni, A. Cortellini, C. Ficorella, R. Chiari, M. Di Maio, J. Aerts, A. Dingemans, L. Nicolardi, A. Caglio, S. Aerts, R. Berardi
Journal: Journal of Thoracic Oncology (2021)
Corrigendum to “Fibrin degradation by rtPA enhances the delivery of nanotherapeutics to A549 tumors in nude mice” [Biomaterials (2016) 63–71]
Authors: Bo Zhang, Ting Jiang, Xiao jian She, Shun Shen, Sheng Wang, Jun Deng, Wei Shi, Heng Mei, Yu Hu, Zhiqing Pang, Xinguo Jiang
Journal: Biomaterials (2021)
P37.11 Assessment of Plasma D-Dimer as a Predictive Biomarker for Treatment Response in Lung Cancer Treated with Radiation Therapy
Authors: A. Chanda, A. Chauhan, P. Kaur, A. Soni, S. Sehgal, A. Khurana, O. Parkash, Y. Verma
Journal: Journal of Thoracic Oncology (2021)
CLO21-030: Does the TP53 Mutation Worsen Prognosis in Carriers of BRCA1/2 Deficiency With Grade 3 Endometrioid Endometrial Carcinoma?
Authors: Aifen Wang, Yong Yin, Jinhua Zhou, Fangrong Shen, Youguo Chen
Journal: Journal of the National Comprehensive Cancer Network (2021)

"CLO21-030: Does the TP53 Mutation Worsen Prognosis in Carriers of BRCA1/2 Deficiency With Grade 3 Endometrioid Endometrial Carcinoma?" published on 17 Mar 2021 by National Comprehensive Cancer Network.
P75.15 Predictive Factors of Survival in Non-Small Cell Lung Cancer Patients Without Durable Response to PD-1/L1 Inhibitors
Authors: Y. Harutani, Y. Ozawa, E. Murakami, K. Sato, J. Oyanagi, H. Akamatsu, S. Teraoka, N. Tokudome, A. Hayata, Y. Koh, H. Ueda, M. Nakanishi, N. Yamamoto
Journal: Journal of Thoracic Oncology (2021)
Abstract 10964: The Biophysical Consequences of Thin Filament Hypertrophic Cardiomyopathy Mutations
Authors: Giuliana Repetti, Christopher Toepfer, Amanda Garfinkel, Victor Bellini, Kallyandra Padilha, Jon Wilcox, Gabriela Venturini, Jonathan Seidman, Christine E Seidman
Journal: Circulation (2019)

It is not yet understood how pathogenic variants in genes of the thin filament cause hypertrophic cardiomyopathy (HCM). Induced pluripotent stem cell-derived cardiomyocytes (IPS-cardiomyocytes) pro...
P13.05 Real-World Treatment Patterns and Sequencing of Immunotherapy and Chemotherapy Based on PD-L1 TPS in European Patients With mNSCLC
Authors: M. Gower, M. Gower, E. Janowicz, D. Anderson, P. Capart, N. Stoyanov, B. Nguyen, A. Combest, R. Ognar
Journal: Journal of Thoracic Oncology (2021)
P48.15 A Case from a Single-Arm, Phase Two, Open Label Study Assessing Sindilimab Plus Metaformin in Chemotherapy Failed PD-L1 Positive Advanced SCLC
Authors: L. Wu, K. Li, B. Chen, W. Peng, J. Wang, M. Jiang, Q. Wang, X. Pu, J. Li, F. Xu, Y. Xu
Journal: Journal of Thoracic Oncology (2021)
Abstract #450: Loss of Tpl2 enhances tumorigenesis and affects tumor phenotype during promotion
Authors: John Simmons, Kathleen DeCicco-Skinner, Jyotsna Pandey, Zhihong Shan, Tejaswini Reddi, Jonathan Wiest
Journal: Cancer Research (2009)

Tpl2 is a serine/threonine protein kinase implicated in the regulation of cellular proliferation, differentiation, and immune response involving chemokine-cytokine production. Tpl2 has been shown to be oncogenic when overexpressed and has been reported in several tumor types. Tpl2 knockout mice do not display an overt phenotype. In the mouse skin carcinogenesis model (also known as the 2-stage chemical carcinogenesis protocol), a single application of phorbol esters (TPA) to mouse skin results in an acute inflammatory response and epidermal hyperplasia. Repeated long-term application of TPA (following carcinogen initiation) leads to tumor formation in susceptible mice. We hypothesized that loss of Tpl2 would lead to a dampened inflammatory response and loss of tumorigenic response. Long-term treatment with TPA for 30 weeks following carcinogen initiation was performed to assess the tumorigenic potential versus wild type controls. This experiment revealed unexpectedly high levels of skin tumor development in the knockout mice after only 9 weeks of TPA application. By 30 weeks, 87% of the knockout animals had a mean of 4 tumors/animal as compared to only 17% of wild type mice with a mean of 1.25 tumors/animal. Surprisingly, histology revealed a large number of the knockout tumors were sebaceous adenomas or a mixed phenotype with aspects of both sebaceous adenoma and squamous carcinoma. The remainder of the knockout tumors were squamous carcincomas or papillomas, while only 1 wildtype tumor had progressed beyond papilloma. We are currently investigating the molecular mechanisms responsible for the highly unusual sebaceous phenotype seen in the knockout tumors. This finding, in addition to enhanced acute inflammation noted in our previous work with short term application of TPA to Tpl2 null mice, point to Tpl2 playing a complex and pleiotropic role in inflammation and tumorigenesis.  Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 450.
DL-3-n-butylphthalide improved physical and learning and memory performance of rodents exposed to acute and chronic hypobaric hypoxia
Authors: Gang Xu, Yi-Kun Shi, Bin-Da Sun, Lu Liu, Guo-Ji E., Shu He, Jian-Yang Zhang, Bao Liu, Qiu Hu, Jian Chen, Yu-Qi Gao, Er-Long Zhang
Journal: Military Medical Research (2021)

Abstract Background Studies have revealed the protective effect of DL-3-n-butylphthalide (NBP) against diseases associated with ischemic hypoxia. However, the role of NBP in animals with hypobaric hypoxia has not been elucidated. This study investigated the effects of NBP on rodents with acute and chronic hypobaric hypoxia. Methods Sprague-Dwaley rats and Kunming mice administered with NBP (0, 60, 120, and 240 mg/kg for rats and 0, 90, 180, and 360 mg/kg for mice) were placed in a hypobaric hypoxia chamber at 10,000 m and the survival percentages at 30 min were determined. Then, the time and distance to exhaustion of drug-treated rodents were evaluated during treadmill running and motor-driven wheel-track treadmill experiments, conducted at 5800 m for 3 days or 20 days, to evaluate changes in physical functions. The frequency of active escapes and duration of active escapes were also determined for rats in a shuttle-box experiment, conducted at 5800 m for 6 days or 27 days, to evaluate changes in learning and memory function. ATP levels were measured in the gastrocnemius muscle and malonaldehyde (MDA), superoxide dismutase (SOD), hydrogen peroxide (H 2 O 2 ), glutathione peroxidase (GSH-Px), and lactate were detected in sera of rats, and routine blood tests were also performed. Results Survival analysis at 10,000 m indicated NBP could improve hypoxia tolerance ability. The time and distance to exhaustion for mice (NBP, 90 mg/kg) and time to exhaustion for rats (NBP, 120 and 240 mg/kg) significantly increased under conditions of acute hypoxia compared with control group. NBP treatment also significantly increased the time to exhaustion for rats when exposed to chronic hypoxia. Moreover, 240 mg/kg NBP significantly increased the frequency of active escapes under conditions of acute hypoxia. Furthermore, the levels of MDA and H 2 O 2 decreased but those of SOD and GSH-Px in the sera of rats increased under conditions of acute and chronic hypoxia. Additionally, ATP levels in the gastrocnemius muscle significantly increased, while lactate levels in sera significantly decreased. Conclusion NBP improved physical and learning and memory functions in rodents exposed to acute or chronic hypobaric hypoxia by increasing their anti-oxidative capacity and energy supply.
Exosome-mediated delivery of an anti-angiogenic peptide inhibits pathological retinal angiogenesis
Authors: Xue Dong, Yi Lei, Zeyang Yu, Tian Wang, Yi Liu, Gang Han, Xiaodan Zhang, Yiming Li, Yinting Song, Heping Xu, Mei Du, Haifang Yin, Xiaohong Wang, Hua Yan
Journal: Theranostics (2021)

Superparamagnetic iron oxide nanoparticle (SPION) tracers possessing long blood circulation time and tailored for magnetic particle imaging (MPI) performance are crucial for the development of this emerging molecular imaging modality.Here, single-core SPION MPI tracers coated with covalently bonded polyethyelene glycol (PEG) brushes were obtained using a semi-batch thermal decomposition synthesis with controlled addition of molecular oxygen, followed by an optimized PEG-silane ligand exchange procedure.The physical and magnetic properties, MPI performance, and blood circulation time of these newly synthesized tracers were compared to those of two commercially available SPIONs that were not tailored for MPI but are used for MPI: ferucarbotran and PEG-coated Synomag ® -D.The new tailored tracer has MPI sensitivity that is ~3-times better than the commercial tracer ferucarbotran and much longer circulation half-life than both commercial tracers (t1/2=6.99 h for the new tracer, vs t1/2=0.59h for ferucarbotran, and t1/2=0.62h for PEG-coated Synomag ® -D).