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Mainlining Databases: Supporting Fast Transactional Workloads on Universal Columnar Data File Formats [article]

Tianyu Li, Matthew Butrovich, Amadou Ngom, Wan Shen Lim, Wes McKinney, Andrew Pavlo
2020 arXiv   pre-print
The proliferation of modern data processing tools has given rise to open-source columnar data formats. The advantage of these formats is that they help organizations avoid repeatedly converting data to a new format for each application. These formats, however, are read-only, and organizations must use a heavy-weight transformation process to load data from on-line transactional processing (OLTP) systems. We aim to reduce or even eliminate this process by developing a storage architecture for
more » ... memory database management systems (DBMSs) that is aware of the eventual usage of its data and emits columnar storage blocks in a universal open-source format. We introduce relaxations to common analytical data formats to efficiently update records and rely on a lightweight transformation process to convert blocks to a read-optimized layout when they are cold. We also describe how to access data from third-party analytical tools with minimal serialization overhead. To evaluate our work, we implemented our storage engine based on the Apache Arrow format and integrated it into the DB-X DBMS. Our experiments show that our approach achieves comparable performance with dedicated OLTP DBMSs while enabling orders-of-magnitude faster data exports to external data science and machine learning tools than existing methods.
arXiv:2004.14471v1 fatcat:cf3fma5wlbamzmxzvvgqg5himi

Hippo/MST blocks breast cancer by downregulating WBP2 oncogene expression via miRNA processor Dicer

Shen Kiat Lim, Hossein Tabatabaeian, Ssu Yi Lu, Shin-Ae Kang, Gopinath Meenakshi Sundaram, Prabha Sampath, Siew Wee Chan, Wan Jin Hong, Yoon Pin Lim
2020 Cell Death and Disease  
Siew Wee Chan and Wan Jin Hong provided reagents, scientific inputs, and technical advice on MST/LATS kinaserelated studies. Shen Kiat Lim wrote the paper.  ...  Shen Kiat Lim, Hossein Tabatabaeian, and Ssu Yi Lu designed and performed the experiments as well as the data. Shin-Ae Kang performed the tumor xenograft study and analysis.  ... 
doi:10.1038/s41419-020-02901-3 pmid:32820148 fatcat:tjiglirihff6xodmgt3ayejm6m

C-reactive Protein, Body Mass Index, and Diabetic Retinopathy

Laurence Shen Lim, E. Shyong Tai, Paul Mitchell, Jie Jin Wang, Wan Ting Tay, Ecosse Lamoureux, Tien Yin Wong
2010 Investigative Ophthalmology and Visual Science  
PURPOSE. C-reactive protein (CRP) is an inflammatory biomarker that may be associated with diabetic retinopathy (DR), but body mass index (BMI) is an important confounder of this relationship. The purpose of this study was to determine the relationship between CRP, BMI, and existing DR. METHODS. This was a population-based, cross-sectional study on 718 persons with diabetes in the Singapore Malay Eye Study (SiMES). Diabetes was defined as random glucose Ն 11.1 mmol/L, on diabetic medication or
more » ... history of physiciandiagnosed diabetes. CRP was measured in frozen plasma. DR was graded from retinal photographs. RESULTS. Higher CRP and BMI were associated with lower prevalence of DR. After adjustment for age, sex, HbA1c level, hypertension, smoking, total cholesterol level, cholesterol-lowering medication, and insulin use, persons with the highest quartiles of CRP were less likely to have any DR (odds ratio [OR] 0.5; 95% CI, 0.3-0.9, comparing the fourth with the first quartile of CRP), vision-threatening DR (OR 0.3; 95% CI, 0.1-0.7), or CSME (OR 0.2; 95% CI, 0.1-0.6). Similarly, persons with the highest quartiles of BMI were less likely to have any DR (OR 0.5; 95% CI, 0.3-0.7), moderate DR (OR 0.4; 95% CI, 0.2-0.7), vision-threatening DR (OR 0.4; 95% CI, 0.1-0.8) or CSME (OR 0.2; 95% CI, 0.0 -1.0). No significant interactions between CRP and BMI on DR were seen. CONCLUSIONS. Persons with diabetes who had higher levels of CRP and BMI were less likely to have DR. Further research is needed to understand the interrelationship role of inflammation, body weight, and microvascular complications. (Invest Ophthalmol Vis Sci.
doi:10.1167/iovs.09-4939 pmid:20805569 fatcat:ueswomgn3zdc3polmweznes7vu

Direct RNA sequencing reveals structural differences between transcript isoforms [article]

Jong Ghut Ashley Aw, Shaun W. Lim, Jia Xu Wang, Yang Shen, Pornchai Kaewsapsak, Eng Piew Louis Kok, Chenhao Li, Boon Hsi Ng, Leah A. Vardy, Meng How Tan, Niranjan Nagarajan, Yue Wan
2020 bioRxiv   pre-print
Acknowledgements We thank members of the Wan lab, Tan lab, Fei Yao, Hwee Meng Loh, Chiea Chuen Khor and Mile Sikic for helpful discussions.  ... 
doi:10.1101/2020.06.11.147223 fatcat:ed4reozhtjehpcrngrauwfjlue

Haem-activated promiscuous targeting of artemisinin in Plasmodium falciparum

Jigang Wang, Chong-Jing Zhang, Wan Ni Chia, Cheryl C. Y. Loh, Zhengjun Li, Yew Mun Lee, Yingke He, Li-Xia Yuan, Teck Kwang Lim, Min Liu, Chin Xia Liew, Yan Quan Lee (+8 others)
2015 Nature Communications  
The mechanism of action of artemisinin and its derivatives, the most potent of the anti-malarial drugs, is not completely understood. Here we present an unbiased chemical proteomics analysis to directly explore this mechanism in Plasmodium falciparum. We use an alkyne-tagged artemisinin analogue coupled with biotin to identify 124 artemisinin covalent binding protein targets, many of which are involved in the essential biological processes of the parasite. Such a broad targeting spectrum
more » ... s the biochemical landscape of the parasite and causes its death. Furthermore, using alkyne-tagged artemisinin coupled with a fluorescent dye to monitor protein binding, we show that haem, rather than free ferrous iron, is predominantly responsible for artemisinin activation. The haem derives primarily from the parasite's haem biosynthesis pathway at the early ring stage and from haemoglobin digestion at the latter stages. Our results support a unifying model to explain the action and specificity of artemisinin in parasite killing.
doi:10.1038/ncomms10111 pmid:26694030 pmcid:PMC4703832 fatcat:vso2zjzkrbdizmom6aoxq4k2za

Vertical Profiling of Aerosol Types Observed across Monsoon Seasons with a Raman Lidar in Penang Island, Malaysia

Wan Shen Hee, Hwee San Lim, Mohd. Zubir Mat Jafri, Simone Lolli, Khor Wei Ying
2016 Aerosol and Air Quality Research  
These largescale meteorological events interact with the unique landsea distribution and create many different types of local weather systems (Lim and Samah, 2004) .  ...  the spring transition, when the Northeast monsoon changed to the Southwest monsoon (April 2014), weak atmospheric circulation promoted the formation of thunderstorms, producing substantial rainfall (Lim  ... 
doi:10.4209/aaqr.2015.07.0450 fatcat:f5726moakve45aw4du7ea62z44

Structure mapping of dengue and Zika viruses reveals new functional long-range interactions [article]

Roland G Huber, Xin Ni Lim, Wy Ching Ng, Adelene Sim, Hui Xian Poh, Yang Shen, Su Ying Lim, Anna Karin Beatrice Sundstrom, Xuyang Sun, Jong Ghut Aw, Horng Khit Too, Peng Hee Boey (+13 others)
2018 bioRxiv   pre-print
Acknowledgements We thank members of the Wan lab, Sessions lab, Ooi lab for discussions. YW is supported by  ... 
doi:10.1101/381368 fatcat:ichyusnocrbrjkgzypkmimyexm

Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes

Sidika Tapsin, Miao Sun, Yang Shen, Huibin Zhang, Xin Ni Lim, Teodorus Theo Susanto, Siwy Ling Yang, Gui Sheng Zeng, Jasmine Lee, Alexander Lezhava, Ee Lui Ang, Lian Hui Zhang (+4 others)
2018 Nature Communications  
Acknowledgements We thank members of the Wan  ...  Since δ is the smallest span of s i , K is bounded between lim δ!0 K À and lim δ!0 K þ and C* is defined by the formula: C Ã ¼ e À2 P 1 k¼1 1 k ðE e λS k ;Sk<0 ð Þ þProb Sk!  ... 
doi:10.1038/s41467-018-03675-1 pmid:29599443 pmcid:PMC5876405 fatcat:jz5iu77u75ghdc6px27d4ltsle

Distribution and Determinants of Ocular Biometric Parameters in an Asian Population: The Singapore Malay Eye Study

Laurence Shen Lim, Seang-Mei Saw, V. Swetha E. Jeganathan, Wan Ting Tay, Tin Aung, Louis Tong, Paul Mitchell, Tien Yin Wong
2010 Investigative Ophthalmology and Visual Science  
PURPOSE. To examine the distribution and systemic determinants of ocular biometry as measured using partial laser interferometry in an adult Asian population. METHODS. A population-based, cross-sectional study of 3280 persons (78.7% participation rate) ages 40 to 80 years, of Malay ethnicity residing in Singapore, was conducted. Axial ocular dimensions, including axial length (AL), anterior chamber depth (ACD), and corneal curvature (CC), were determined with partial laser interferometry.
more » ... ipants had a comprehensive interview and a standardized examination. RESULTS. After 492 persons were excluded who had undergone cataract surgery, data on 2788 subjects were available. The mean AL, ACD, and CC were 23.55, 3.10, and 7.65 mm, respectively. AL and ACD decreased with increasing age. In multivariate models that adjusted for age, sex, education, height, weight, number of reading hours, diabetes, and current smoking, longer AL was associated with being male, height, increasing weight, higher education levels, and total reading hours. Increasing CC was associated with greater age and greater height and weight after multivariable adjustment. CONCLUSIONS. Age, sex, and stature were the most consistent predictors of the results of ocular biometry in the Singapore Malay adult population. (Invest Ophthalmol Vis Sci.
doi:10.1167/iovs.09-3553 pmid:19684013 fatcat:dytinfznmnhejmkjko6adbes3e

Monomodality versus Combined Therapy in Optic Pathway Gliomas—20-Year Experience from a Singapore Children's Hospital

Jia Xu Lim, Enrica E.K. Tan, Lee Ping Ng, Wan Tew Seow, Kenneth T.E. Chang, Ru Xin Wong, Wen Shen Looi, David C.Y. Low, Sharon Y.Y. Low
2022 Frontiers in Surgery  
IntroductionThe treatment of pediatric optic pathway gliomas (OPG) is challenging. At present, most centers provide individualized treatment to maximize progression free survival (PFS) and minimize morbidity. We aim to report our experience in the management of pediatric OPG, and investigate factors associated with an increased duration of remission after treatment.MethodsThis is a single-institution study approved by the hospital ethics board. A retrospective review of consecutive OPGs managed
more » ... from 2000 to 2020 was performed. Patients were divided into those managed with monomodality treatment (MT) and those who received combined therapy (CT). MT included various forms of surgery, chemotherapy and radiotherapy given alone, while CT involves a combination of surgery and adjuvant chemotherapy and/or radiotherapy.ResultsTwenty-two patients were selected for this study. They had 40 treatment cycles; and a total follow up duration of 194.8 patient-years. Most of them were male (63.6%) and presented with visual deficits (72.7%). The mean age at initial presentation was 65 months and majority (86.4%) had their tumors arising directly from the optic chiasm, with 77.3% with hypothalamic extension. One patient had Neurofibromatosis type I (4.5%). The most common histological diagnosis was pilocytic astrocytoma (90.9%), followed by pilomyxoid astrocytoma (9.1%). The 5- and 10- year PFS were 46.2% and 36.4% respectively, while the 5- and 10-year OS were both 100%. When accounting for treatment type, there were 24 treatment cycles with MT (60.0%) and 16 CT (40.0%). After adjustment, treatments with MT were shown to have a shorter mean duration of remission (MT: 45 ± 49, CT: 84 ± 79 months; p = 0.007). Cox regression curve plotted after adjusting for patient's age at treatment demonstrated a significantly longer PFS in the CT group (p = 0.037).ConclusionsOur results suggest a significant survival benefit of CT over MT for affected patients due to the prolonged the duration of disease remission, for both primary and subsequent treatments. Nonetheless, we acknowledge that our study reflects the outcomes of treatment strategies that have evolved over time. We emphasize the need for collective efforts from a dedicated multidisciplinary team and international collaborations for better disease understanding.
doi:10.3389/fsurg.2022.827675 pmid:35586500 pmcid:PMC9108767 fatcat:rskkbhyvdfgg5ceg3bsrcnmn7u

Metabolic Reprogramming of GMP Grade Cord Tissue Derived Mesenchymal Stem Cells Enhances Their Suppressive Potential in GVHD

Mayela Mendt, May Daher, Rafet Basar, Mayra Shanley, Bijender Kumar, Francesca Lim Wei Inng, Sunil Acharya, Hila Shaim, Natalie Fowlkes, Jamie P. Tran, Elif Gokdemir, Nadima Uprety (+33 others)
2021 Frontiers in Immunology  
Acute graft-vs.-host (GVHD) disease remains a common complication of allogeneic stem cell transplantation with very poor outcomes once the disease becomes steroid refractory. Mesenchymal stem cells (MSCs) represent a promising therapeutic approach for the treatment of GVHD, but so far this strategy has had equivocal clinical efficacy. Therapies using MSCs require optimization taking advantage of the plasticity of these cells in response to different microenvironments. In this study, we aimed to
more » ... optimize cord blood tissue derived MSCs (CBti MSCs) by priming them using a regimen of inflammatory cytokines. This approach led to their metabolic reprogramming with enhancement of their glycolytic capacity. Metabolically reprogrammed CBti MSCs displayed a boosted immunosuppressive potential, with superior immunomodulatory and homing properties, even after cryopreservation and thawing. Mechanistically, primed CBti MSCs significantly interfered with glycolytic switching and mTOR signaling in T cells, suppressing T cell proliferation and ensuing polarizing toward T regulatory cells. Based on these data, we generated a Good Manufacturing Process (GMP) Laboratory protocol for the production and cryopreservation of primed CBti MSCs for clinical use. Following thawing, these cryopreserved GMP-compliant primed CBti MSCs significantly improved outcomes in a xenogenic mouse model of GVHD. Our data support the concept that metabolic profiling of MSCs can be used as a surrogate for their suppressive potential in conjunction with conventional functional methods to support their therapeutic use in GVHD or other autoimmune disorders.
doi:10.3389/fimmu.2021.631353 pmid:34017325 pmcid:PMC8130860 fatcat:qnqbgb6vabbhda2ef2grhfqvxy

European polygenic risk score for prediction of breast cancer shows similar performance in Asian women

Weang-Kee Ho, Min-Min Tan, Nasim Mavaddat, Mei-Chee Tai, Shivaani Mariapun, Jingmei Li, Peh-Joo Ho, Joe Dennis, Jonathan P. Tyrer, Manjeet K. Bolla, Kyriaki Michailidou, Qin Wang (+51 others)
2020 Nature Communications  
Polygenic risk scores (PRS) have been shown to predict breast cancer risk in European women, but their utility in Asian women is unclear. Here we evaluate the best performing PRSs for European-ancestry women using data from 17,262 breast cancer cases and 17,695 controls of Asian ancestry from 13 case-control studies, and 10,255 Chinese women from a prospective cohort (413 incident breast cancers). Compared to women in the middle quintile of the risk distribution, women in the highest 1% of PRS
more » ... istribution have a ~2.7-fold risk and women in the lowest 1% of PRS distribution has ~0.4-fold risk of developing breast cancer. There is no evidence of heterogeneity in PRS performance in Chinese, Malay and Indian women. A PRS developed for European-ancestry women is also predictive of breast cancer risk in Asian women and can help in developing risk-stratified screening programmes in Asia.
doi:10.1038/s41467-020-17680-w pmid:32737321 fatcat:npcn7cqby5bjfcgtvudwjxvi2i

CIS checkpoint deletion enhances the fitness of cord blood derived natural killer cells transduced with a chimeric antigen receptor [article]

Katy Rezvani, May Daher, Rafet Basar, Elif Gokdemir, Natalia Baran, Nadima Uprety, Mayela Mendt, Lucila Kerbauy, Mayra Hernandez Sanabria, Nobuhiko Imahashi, Ana Nunez, Li Li (+42 others)
2020 bioRxiv   pre-print
Immune checkpoint therapy has produced remarkable improvements in the outcome for certain cancers. To broaden the clinical impact of checkpoint targeting, we devised a strategy that couples targeting of the cytokine-inducible SH2-containing (CIS) protein, a key negative regulator of interleukin (IL)-15 signaling, with chimeric antigen receptor (CAR) engineering of natural killer (NK) cells. This combined strategy boosted NK cell effector function through enhancing the Akt/mTORC1 axis and c-MYC
more » ... ignaling, resulting in increased aerobic glycolysis. When tested in a lymphoma mouse model, this combined approach improved NK cell anti-tumor activity more than either alteration alone, eradicating lymphoma xenografts without signs of any measurable toxicity. We conclude that combining CIS checkpoint deletion with CAR engineering promotes the metabolic fitness of NK cells in an otherwise suppressive tumor microenvironment. This approach, together with the prolonged survival afforded by CAR modification, represents a promising milestone in the development of the next generation of NK cells for cancer immunotherapy.
doi:10.1101/2020.03.29.014472 fatcat:gdxdwrkrhvg3xhnfyluupvhhgy

Page 215 of Perspectives in Public Health Vol. 122, Issue 4 [page]

2002 Perspectives in Public Health  
Blood circulation Jiao Nang (Tiansu) capsules Weight loss Kang Gu Che Sheng Wan pills Neck spondylitis and neck circulation Kintop capsules Weight loss Qian Er capsules Weight loss Shen Qi Da Bu Wan pills  ...  She had put on ; 1 x her recent pregnancy and was lim sum ] nming products the unnamed vellow tablets.  ... 


2016 Heterocycles  
Concise Synthesis and Biological Evaluation of Chalcone Derivatives Bearing N-Heterocyclic Moieties Zewei Mao, Xi Zheng, Yuping Lin, Yan Qi, Chunyan Hu, Chunping Wan,* and Gaoxiong Rao* Chalcone  ...  Hydantoin Twin-Drug Symmetrical Bivalent Molecule Structure-Activity Relationship Antibacterial Activity Synthesis and Antileukemic Activity of New Fluorinated 5- Aza-9-deazapurines Felicia Phei Lin Lim  ... 
doi:10.3987/contents-16-9206 fatcat:yzxuiwsyujh75m3t6ekxybwp5q
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